Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks

NASA Astrophysics Data System (ADS)

Fahrenthold, Eric; Bass, Joseph

2015-06-01

Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.

Differential effects of genetically distinct mechanisms of elevating amylose on barley starch characteristics.

PubMed

Regina, Ahmed; Blazek, Jaroslav; Gilbert, Elliot; Flanagan, Bernadine M; Gidley, Michael J; Cavanagh, Colin; Ral, Jean-Philippe; Larroque, Oscar; Bird, Anthony R; Li, Zhongyi; Morell, Matthew K

2012-07-01

The relationships between starch structure and functionality are important in underpinning the industrial and nutritional utilisation of starches. In this work, the relationships between the biosynthesis, structure, molecular organisation and functionality have been examined using a series of defined genotypes in barley with low (<20%), standard (20-30%), elevated (30-50%) and high (>50%) amylose starches. A range of techniques have been employed to determine starch physical features, higher order structure and functionality. The two genetic mechanisms for generating high amylose contents (down-regulation of branching enzymes and starch synthases, respectively) yielded starches with very different amylopectin structures but similar gelatinisation and viscosity properties driven by reduced granular order and increased amylose content. Principal components analysis (PCA) was used to elucidate the relationships between genotypes and starch molecular structure and functionality. Parameters associated with granule order (PC1) accounted for a large percentage of the variance (57%) and were closely related to amylose content. Parameters associated with amylopectin fine structure accounted for 18% of the variance but were less closely aligned to functionality parameters. Copyright © 2012 Elsevier Ltd. All rights reserved.

Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

NASA Astrophysics Data System (ADS)

Stepanova, L. V.

2017-12-01

Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

Molecular Static Third-Order Polarizabilities of Carbon-Cage Fullerene and Their Correlation with Three Geometric Properties: Symmetry, Aromaticity, and Size

NASA Technical Reports Server (NTRS)

Moore, C. E.; Cardelino, B. H.; Frazier, D. O.; Niles, J.; Wang, X.-Q.

1998-01-01

The static third-order polarizabilities (gamma) of C60, C70, five isomers of C78 and two isomers of C84 were analyzed in terms of three properties, from a geometric point of view: symmetry, aromaticity and size. The polarizability values were based on the finite field approximation using a semiempirical Hamiltonian (AM1) and applied to molecular structures obtained from density functional theory calculations. Symmetry was characterized by the molecular group order. The selection of 6-member rings as aromatic was determined from an analysis of bond lengths. Maximum interatomic distance and surface area were the parameters considered with respect to size. Based on triple linear regression analysis, it was found that the static linear polarizability (alpha) and gamma in these molecules respond differently to geometrical properties: alpha depends almost exclusively on surface area while gamma is affected by a combination of number of aromatic rings, length and group order, in decreasing importance. In the case of alpha, valence electron contributions provide the same information as all-electron estimates. For gamma, the best correlation coefficients are obtained when all-electron estimates are used and when the dependent parameter is ln(gamma) instead of gamma.

Modeling the [NTf2] pyridinium ionic liquids family and their mixtures with the soft statistical associating fluid theory equation of state.

PubMed

Oliveira, M B; Llovell, F; Coutinho, J A P; Vega, L F

2012-08-02

In this work, the soft statistical associating fluid theory (soft-SAFT) equation of state (EoS) has been used to provide an accurate thermodynamic characterization of the pyridinium-based family of ionic liquids (ILs) with the bis(trifluoromethylsulfonyl)imide anion [NTf(2)](-). On the basis of recent molecular simulation studies for this family, a simple molecular model was proposed within the soft-SAFT EoS framework. The chain length value was transferred from the equivalent imidazolium-based ILs family, while the dispersive energy and the molecular parameters describing the cation-anion interactions were set to constant values for all of the compounds. With these assumptions, an appropriate set of molecular parameters was found for each compound fitting to experimental temperature-density data at atmospheric pressure. Correlations for the nonconstant parameters (describing the volume of the IL) with the molecular weight were established, allowing the prediction of the parameters for other pyridiniums not included in the fitting. Then, the suitability of the proposed model and its optimized parameters were tested by predicting high-pressure densities and second-order thermodynamic derivative properties such as isothermal compressibilities of selected [NTf(2)] pyridinium ILs, in a large range of thermodynamic conditions. The surface tension was also provided using the density gradient theory coupled to the soft-SAFT equation. Finally, the soft-SAFT EoS was applied to describe the phase behavior of several binary mixtures of [NTf(2)] pyridinium ILs with carbon dioxide, sulfur dioxide, and water. In all cases, a temperature-independent binary parameter was enough to reach quantitative agreement with the experimental data. The description of the solubility of CO(2) in these ILs also allowed identification of a relation between the binary parameter and the molecular weight of the ionic liquid, allowing the prediction of the CO(2) + C(12)py[NTf(2)] mixture. The good agreement with the experimental data shows the excellent ability of the soft-SAFT EoS to describe the thermophysical properties of ILs as well as their phase behavior. Results prove that this equation of state can be a valuable tool to assist the design of ILs (in what concerns cation and anion selection) in order to obtain ILs with the desired properties and, consequently, enhancing their potential industrial applications.

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Exploring the site-selective binding of jatrorrhizine to human serum albumin: spectroscopic and molecular modeling approaches.

PubMed

Mi, Ran; Hu, Yan-Jun; Fan, Xiao-Yang; Ouyang, Yu; Bai, Ai-Min

2014-01-03

This paper exploring the site-selective binding of jatrorrhizine to human serum albumin (HSA) under physiological conditions (pH=7.4). The investigation was carried out using fluorescence spectroscopy, UV-vis spectroscopy, and molecular modeling. The results of fluorescence quenching and UV-vis absorption spectra experiments indicated the formation of the complex of HSA-jatrorrhizine. Binding parameters calculating from Stern-Volmer method and Scatchard method were calculated at 298, 304 and 310 K, with the corresponding thermodynamic parameters ΔG, ΔH and ΔS as well. Binding parameters calculating from Stern-Volmer method and Scatchard method showed that jatrorrhizine bind to HSA with the binding affinities of the order 10(4) L mol(-1). The thermodynamic parameters studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the electrostatic interactions play a major role for jatrorrhizine-HSA association. Site marker competitive displacement experiments and molecular modeling calculation demonstrating that jatrorrhizine is mainly located within the hydrophobic pocket of the subdomain IIIA of HSA. Furthermore, the synchronous fluorescence spectra suggested that the association between jatrorrhizine and HSA changed molecular conformation of HSA. Copyright © 2013. Published by Elsevier B.V.

A cobalt (II) complex with 6-methylpicolinate: Synthesis, characterization, second- and third-order nonlinear optical properties, and DFT calculations

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avcı, Davut; Tamer, Ömer; Atalay, Yusuf; Şahin, Onur

2016-11-01

A cobalt(II) complex of 6-methylpicolinic acid, [Co(6-Mepic)2(H2O)2]·2H2O, was prepared and fully determined by single crystal X-ray crystal structure analysis as well as FT-IR, FT-Raman. UV-vis spectra were recorded within different solvents, to illustrate electronic transitions and molecular charge transfer within complex 1. The coordination sphere of complex 1 is a distorted octahedron according to single crystal X-ray results. Moreover, DFT (density functional theory) calculations with HSEH1PBE/6-311 G(d,p) level were carried out to back up the experimental results, and form base for future work in advanced level. Hyperconjugative interactions, intramolecular charge transfer (ICT), molecular stability and bond strength were researched by the using natural bond orbital (NBO) analysis. X-ray and NBO analysis results demonsrate that O-H···O hydrogen bonds between the water molecules and carboxylate oxygen atoms form a 2D supramolecular network, and also adjacent 2D networks connected by C-H···π and π···π interactions to form a 3D supramolecular network. Additionally, the second- and third-order nonlinear optical parameters of complex 1 were computed at DFT/HSEH1PBE/6-311 G(d,p) level. The refractive index (n) was calculated by using the Lorentz-Lorenz equation in order to investigate polarization behavior of complex 1 in different solvent polarities. The first-order static hyperpolarizability (β) value is found to be lower than pNA value because of the inversion symmetry around Co (II). But the second-order static hyperpolarizability (γ) value is 2.45 times greater than pNA value (15×10-30 esu). According to these results, Co(II) complex can be considered as a candidate to NLO material. Lastly molecular electrostatic potential (MEP), frontier molecular orbital energies and related molecular parameters for complex 1 were evaluated.

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

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

Liu, Qing; Shi, Chaowei; Yu, Lu

Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in amore » defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.« less

Phase behavior and orientational ordering in block copolymers doped with anisotropic nanoparticles

NASA Astrophysics Data System (ADS)

Osipov, M. A.; Gorkunov, M. V.; Berezkin, A. V.; Kudryavtsev, Y. V.

2018-04-01

A molecular field theory and coarse-grained computer simulations with dissipative particle dynamics have been used to study the spontaneous orientational ordering of anisotropic nanoparticles in the lamellar and hexagonal phases of diblock copolymers and the effect of nanoparticles on the phase behavior of these systems. Both the molecular theory and computer simulations indicate that strongly anisotropic nanoparticles are ordered orientationally mainly in the boundary region between the domains and the nematic order parameter possesses opposite signs in adjacent domains. The orientational order is induced by the boundary and by the interaction between nanoparticles and the monomer units in different domains. In simulations, sufficiently long and strongly selective nanoparticles are ordered also inside the domains. The nematic order parameter and local concentration profiles of nanoparticles have been calculated numerically using the model of a nanoparticle with two interaction centers and also determined using the results of computer simulations. A number of phase diagrams have been obtained which illustrate the effect of nanoparticle selectivity and molar fraction of the stability ranges of various phases. Different morphologies have been identified by analyzing the static structure factor and a phase diagram has been constructed in coordinates' nanoparticle concentration-copolymer composition. Orientational ordering of even a small fraction of nanoparticles may result in a significant increase of the dielectric anisotropy of a polymer nanocomposite, which is important for various applications.

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid Sb from 913 K to 1193 K

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; Li, Y. D.; Kong, Xiang-Shan; Liu, C. S.

2013-02-01

Ab initio molecular dynamics simulations on liquid Sb have been carried out at five different temperatures from 913 K to 1193 K. We have investigated the temperature dependence of structure properties including structural factor S(Q), pair correlation function g(r), bond-angle distribution function g3(θ), cluster properties and bond order parameter Q4 and Q6. A shoulder was reproduced in the high wave number side of the first peak in the S(Q) implying that the residual structure units of crystalline Sb remain in liquid Sb. There is a noticeable bend at around 1023 K in the temperature dependence of the first-peak height of S(Q), the cluster properties and bond order parameter Q4, respectively, indicating that an abnormal structural change may occur at 973-1023 K.

Transition to organized behavior on suspensions of concentrated bacteria

NASA Astrophysics Data System (ADS)

Ganguly, Sujoy; Cisneros, Luis; Kessler, John; Goldstein, Raymond

2008-11-01

Concentrated populations of the swimming bacterium Bacillus subtilis develop a collective phase, the Zooming BioNematic, that exhibits large-scale coherence analogous to the molecular alignment of nematic liquid crystals. Bacterial suspensions were prepared in order to experimentally measure the transition to organized behavior as a function of the cell number concentration. PIV analysis was used to obtain cell velocities and define an order parameter in order to characterize the dynamics of the system.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

High Resolution Spectroscopy to Support Atmospheric Measurements

NASA Technical Reports Server (NTRS)

Venkataraman, Malathy Devi

2003-01-01

Spectroscopic parameters (such as line position, intensity, broadening and shifting coefficients and their temperature dependences, line mixing coefficients etc.) for various molecular species of atmospheric interest are determined. In order to achieve these results, infrared spectra of several molecular bands are obtained using high-resolution recording instruments such as tunable diode laser spectrometer and Fourier transform spectrometers. Using sophisticated analysis routines (Multispectrum nonlinear least squares technique) these high-resolution infrared spectra are processed to determine the various spectral line parameters that are cited above. Spectra were taken using the McMath-Pierce Fourier transform spectrometer (FTS) at the National Solar Observatory on Kitt Peak, Arizona as well as the Bruker FTS at the Pacific Northwest National Laboratory (PNNL) at Richland, Washington. Most of the spectra are acquired not only at room temperature, but also at several different cold temperatures. This procedure is necessary to study the variation of the spectral line parameters as a function of temperature in order to simulate the Earth's and other planetary atmospheric environments. Depending upon the strength or weakness of the various bands recorded and analyzed, the length(s) of the absorption cells in which the gas samples under study are kept varied from a few centimeters up to several meters and the sample temperatures varied from approximately +30 C to -63 C. Research on several infrared bands of various molecular species and their isotopomers are undertaken. Those studies are briefly described.

Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

PubMed Central

Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

2008-01-01

Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy

PubMed Central

Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K.; Sud, Sudha; Stringer, Kathleen A.; Rosania, Gus R.

2017-01-01

Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals. PMID:28270989

Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy.

PubMed

Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K; Sud, Sudha; Stringer, Kathleen A; Rosania, Gus R

2017-02-01

Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals.

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Todd, B. D.; Sadus, Richard J.

2004-12-01

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.

Evidence-Based Diagnostic Algorithm for Glioma: Analysis of the Results of Pathology Panel Review and Molecular Parameters of EORTC 26951 and 26882 Trials.

PubMed

Kros, Johan M; Huizer, Karin; Hernández-Laín, Aurelio; Marucci, Gianluca; Michotte, Alex; Pollo, Bianca; Rushing, Elisabeth J; Ribalta, Teresa; French, Pim; Jaminé, David; Bekka, Nawal; Lacombe, Denis; van den Bent, Martin J; Gorlia, Thierry

2015-06-10

With the rapid discovery of prognostic and predictive molecular parameters for glioma, the status of histopathology in the diagnostic process should be scrutinized. Our project aimed to construct a diagnostic algorithm for gliomas based on molecular and histologic parameters with independent prognostic values. The pathology slides of 636 patients with gliomas who had been included in EORTC 26951 and 26882 trials were reviewed using virtual microscopy by a panel of six neuropathologists who independently scored 18 histologic features and provided an overall diagnosis. The molecular data for IDH1, 1p/19q loss, EGFR amplification, loss of chromosome 10 and chromosome arm 10q, gain of chromosome 7, and hypermethylation of the promoter of MGMT were available for some of the cases. The slides were divided in discovery (n = 426) and validation sets (n = 210). The diagnostic algorithm resulting from analysis of the discovery set was validated in the latter. In 66% of cases, consensus of overall diagnosis was present. A diagnostic algorithm consisting of two molecular markers and one consensus histologic feature was created by conditional inference tree analysis. The order of prognostic significance was: 1p/19q loss, EGFR amplification, and astrocytic morphology, which resulted in the identification of four diagnostic nodes. Validation of the nodes in the validation set confirmed the prognostic value (P < .001). We succeeded in the creation of a timely diagnostic algorithm for anaplastic glioma based on multivariable analysis of consensus histopathology and molecular parameters. © 2015 by American Society of Clinical Oncology.

Conformational Entropy of FK506 Binding to FKBP12 Determined by Nuclear Magnetic Resonance Relaxation and Molecular Dynamics Simulations.

PubMed

Solomentsev, Gleb; Diehl, Carl; Akke, Mikael

2018-03-06

FKBP12 (FK506 binding protein 12 kDa) is an important drug target. Nuclear magnetic resonance (NMR) order parameters, describing amplitudes of motion on the pico- to nanosecond time scale, can provide estimates of changes in conformational entropy upon ligand binding. Here we report backbone and methyl-axis order parameters of the apo and FK506-bound forms of FKBP12, based on 15 N and 2 H NMR relaxation. Binding of FK506 to FKBP12 results in localized changes in order parameters, notably for the backbone of residues E54 and I56 and the side chains of I56, I90, and I91, all positioned in the binding site. The order parameters increase slightly upon FK506 binding, indicating an unfavorable entropic contribution to binding of TΔ S = -18 ± 2 kJ/mol at 293 K. Molecular dynamics simulations indicate a change in conformational entropy, associated with all dihedral angles, of TΔ S = -26 ± 9 kJ/mol. Both these values are significant compared to the total entropy of binding determined by isothermal titration calorimetry and referenced to a reactant concentration of 1 mM ( TΔ S = -29 ± 1 kJ/mol). Our results reveal subtle differences in the response to ligand binding compared to that of the previously studied rapamycin-FKBP12 complex, despite the high degree of structural homology between the two complexes and their nearly identical ligand-FKBP12 interactions. These results highlight the delicate dependence of protein dynamics on drug interactions, which goes beyond the view provided by static structures, and reinforce the notion that protein conformational entropy can make important contributions to the free energy of ligand binding.

Molecular ordering and molecular dynamics in isotactic-polypropylene characterized by solid state NMR.

PubMed

Miyoshi, Toshikazu; Mamun, Al; Hu, Wei

2010-01-14

The order-disorder phenomenon of local packing structures, space heterogeneity, and molecular dynamics and average lamellar thickness, , of the alpha form of isotactic polypropylene (iPP) crystallized at various supercooling temperatures, DeltaT, are investigated by solid-state (SS) NMR and SAXS, respectively. increases with lowering DeltaT, and extrapolations of (-1) versus averaged melting point, , gives an equilibrium melting temperature, T(m)(0) = 457 +/- 4 K. High-power TPPM decoupling with a field strength of 110 kHz extremely improves (13)C high-resolution SS-NMR spectral resolution of the ordered crystalline signals at various DeltaT. A high-resolution (13)C SS-NMR spectrum combined with a conventional spin-lattice relaxation time in the rotating frame (T(1rhoH)) filter easily accesses an order-disorder phenomenon for upward and downward orientations of stems and their packing in the crystalline region. It is found that ordered packing fraction, f(order), increases with lowering DeltaT and reaches a maximum value of 62% at DeltaT = 34 K. The ordering phenomenon of stem packing indicates that chain-folding direction changes from random in the disordered packing to order in the ordered packing along the a sin theta axis under a hypothesis of adjacent re-entry structures. It is also found that f(order) significantly increases prior to enhancement of lamellar thickness. Additionally, annealing experiments indicate that is significantly enhanced after a simultaneous process of partial melting and recrystallization/reorganization into the ordered packing at annealing temperature >/=423 K. Furthermore, the center-bands only detection of exchange (CODEX) NMR method demonstrates that time-kinetic parameters of helical jump motions are highly influenced by DeltaT. These dynamic constraints are interpreted in terms of increment of and packing ordering. Through these new results related to molecular structures and dynamics, roles of polymer chain trajectory and molecular dynamics for the lamellar thickening process are discussed.

Submillisecond elastic recoil reveals molecular origins of fibrin fiber mechanics.

PubMed

Hudson, Nathan E; Ding, Feng; Bucay, Igal; O'Brien, E Timothy; Gorkun, Oleg V; Superfine, Richard; Lord, Susan T; Dokholyan, Nikolay V; Falvo, Michael R

2013-06-18

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin's elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin's mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

PubMed Central

Hudson, Nathan E.; Ding, Feng; Bucay, Igal; O’Brien, E. Timothy; Gorkun, Oleg V.; Superfine, Richard; Lord, Susan T.; Dokholyan, Nikolay V.; Falvo, Michael R.

2013-01-01

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers. PMID:23790375

A theoretical-electron-density databank using a model of real and virtual spherical atoms.

PubMed

Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

2017-08-01

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

Crystal structure, vibrational spectra and DFT studies of hydrogen bonded 1,2,4-triazolium hydrogenselenate

NASA Astrophysics Data System (ADS)

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

2017-10-01

The new hydrogen bonded molecular complex 1,2,4-triazolium hydrogenselenate (THS) is prepared by the reaction of 1H-1,2,4-triazole and selenic acid. This complex is stabilised by N-H⋯O and C-H⋯O hydrogen bonding and electrostatic attractive forces between 1H and 1,2,4-triazolium cations and hydrogen selenate anions. The XRD studies revealed that intermolecular proton transfer occur from selenic acid to 1H-1,2,4-triazole molecule, results in the formation of 1,2,4-triazolium hydrogenselenate which contains 1,2,4-triazolium cations and hydrogenselenate anions. The molecular structure of THS crystal has also been optimised by using Density Functional Theory (DFT) using B3LYP/cc-pVTZ and B3LYP/6-311++G** methods in order to find the whole characteristics of the molecular complex. The theoretical structural parameters such as bond length, bond angle and dihedral angle determined by DFT methods are well agreed with the XRD parameters. The atomic charges and thermodynamic properties are also calculated and analysed. The energies of frontier molecular orbitals HOMO, LUMO, HOMO-1, LUMO+1 and LUMO-HUMO energy gap are calculated to understand the kinetic stability and chemical reactivity of the molecular complex. The natural bond orbital analysis (NBO) has been performed in order to study the intramolecular bonding interactions and delocalisation of electrons. These intra molecular charge transfer may induce biological activities such as antimicrobials, antiinflammatory, antifungal etc. The complete vibrational assignments of THS have been performed by using FT-IR and FT-Raman spectra.

Bubble nucleation in simple and molecular liquids via the largest spherical cavity method

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

Gonzalez, Miguel A., E-mail: m.gonzalez12@imperial.ac.uk; Department of Chemistry, Imperial College London, London SW7 2AZ; Abascal, José L. F.

2015-04-21

In this work, we propose a methodology to compute bubble nucleation free energy barriers using trajectories generated via molecular dynamics simulations. We follow the bubble nucleation process by means of a local order parameter, defined by the volume of the largest spherical cavity (LSC) formed in the nucleating trajectories. This order parameter simplifies considerably the monitoring of the nucleation events, as compared with the previous approaches which require ad hoc criteria to classify the atoms and molecules as liquid or vapor. The combination of the LSC and the mean first passage time technique can then be used to obtain themore » free energy curves. Upon computation of the cavity distribution function the nucleation rate and free-energy barrier can then be computed. We test our method against recent computations of bubble nucleation in simple liquids and water at negative pressures. We obtain free-energy barriers in good agreement with the previous works. The LSC method provides a versatile and computationally efficient route to estimate the volume of critical bubbles the nucleation rate and to compute bubble nucleation free-energies in both simple and molecular liquids.« less

Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations.

PubMed

Okimoto, Noriaki; Suenaga, Atsushi; Taiji, Makoto

2017-11-01

In computational drug design, ranking a series of compound analogs in a manner that is consistent with experimental affinities remains a challenge. In this study, we evaluated the prediction of protein-ligand binding affinities using steered molecular dynamics simulations. First, we investigated the appropriate conditions for accurate predictions in these simulations. A conic harmonic restraint was applied to the system for efficient sampling of work values on the ligand unbinding pathway. We found that pulling velocity significantly influenced affinity predictions, but that the number of collectable trajectories was less influential. We identified the appropriate pulling velocity and collectable trajectories for binding affinity predictions as 1.25 Å/ns and 100, respectively, and these parameters were used to evaluate three target proteins (FK506 binding protein, trypsin, and cyclin-dependent kinase 2). For these proteins using our parameters, the accuracy of affinity prediction was higher and more stable when Jarzynski's equality was employed compared with the second-order cumulant expansion equation of Jarzynski's equality. Our results showed that steered molecular dynamics simulations are effective for predicting the rank order of ligands; thus, they are a potential tool for compound selection in hit-to-lead and lead optimization processes.

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

NASA Astrophysics Data System (ADS)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

FAST TRACK COMMUNICATION: Ferroelectricity in low-symmetry biaxial nematic liquid crystals

NASA Astrophysics Data System (ADS)

Osipov, Mikhail A.; Gorkunov, Maxim V.

2010-09-01

Order parameters and phenomenological theory for both high- and low-symmetry biaxial nematic phases are presented and it is predicted that the chiral low-symmetry biaxial phase must be ferroelectric. This conclusion is based on general symmetry arguments and on the results of the Landau-de Gennes theory. The microscopic mechanism of the ferroelectric ordering in this chiral biaxial phase is illustrated using a simple molecular model based on dispersion interactions between biaxial molecules of low symmetry. Similar to the chiral smectic C* phase, the ferroelectricity in the chiral biaxial nematic phase is improper, i.e., polarization is not a primary order parameter and is not determined by dipolar interactions. Ferroelectric ordering in biaxial nematics may be found, in principle, in materials composed of chiral analogues of the tetrapod molecules which are known to exhibit biaxial phases.

Banding of NMR-derived Methyl Order Parameters: Implications for Protein Dynamics

PubMed Central

Sharp, Kim A.; Kasinath, Vignesh; Wand, A. Joshua

2014-01-01

Our understanding of protein folding, stability and function has begun to more explicitly incorporate dynamical aspects. Nuclear magnetic resonance has emerged as a powerful experimental method for obtaining comprehensive site-resolved insight into protein motion. It has been observed that methyl-group motion tends to cluster into three “classes” when expressed in terms of the popular Lipari-Szabo model-free squared generalized order parameter. Here the origins of the three classes or bands in the distribution of order parameters are examined. As a first step, a Bayesian based approach, which makes no a priori assumption about the existence or number of bands, is developed to detect the banding of O2axis values derived either from NMR experiments or molecular dynamics simulations. The analysis is applied to seven proteins with extensive molecular dynamics simulations of these proteins in explicit water to examine the relationship between O2 and fine details of the motion of methyl bearing side chains. All of the proteins studied display banding, with some subtle differences. We propose a very simple yet plausible physical mechanism for banding. Finally, our Bayesian method is used to analyze the measured distributions of methyl group motions in the catabolite activating protein and several of its mutants in various liganded states and discuss the functional implications of the observed banding to protein dynamics and function. PMID:24677353

Theoretical study on the molecular structure and vibrational properties, NBO and HOMO-LUMO analysis of the POX3 (X = F, Cl, Br, I) series of molecules

NASA Astrophysics Data System (ADS)

Galván, Jorge E.; Gil, Diego M.; Lanús, Hernán E.; Altabef, Aida Ben

2015-02-01

The fourth member of the series of compounds of the type POX3 with X = I was synthesized and characterized by infrared spectroscopy. The geometrical parameters and vibrational properties of POX3 (X = F, Cl, Br, I) molecules were investigated theoretically by means DFT and ab initio methods. Available geometrical and vibrational data were used together with theoretical calculations in order to obtain a set of scaled force constants. The observed trends in geometrical parameters are analyzed and compared with those obtained in a previous work for the VOX3 (X = F, Cl, Br, I) series of compounds. NBO analysis was performed in order to know the hyper-conjugative interactions that favor one structure over another. The molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, chemical hardness, softness and global electrophilicity index have been deduced from HOMO-LUMO analysis.

Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations.

PubMed

Sultan, Mohammad M; Kiss, Gert; Shukla, Diwakar; Pande, Vijay S

2014-12-09

Given the large number of crystal structures and NMR ensembles that have been solved to date, classical molecular dynamics (MD) simulations have become powerful tools in the atomistic study of the kinetics and thermodynamics of biomolecular systems on ever increasing time scales. By virtue of the high-dimensional conformational state space that is explored, the interpretation of large-scale simulations faces difficulties not unlike those in the big data community. We address this challenge by introducing a method called clustering based feature selection (CB-FS) that employs a posterior analysis approach. It combines supervised machine learning (SML) and feature selection with Markov state models to automatically identify the relevant degrees of freedom that separate conformational states. We highlight the utility of the method in the evaluation of large-scale simulations and show that it can be used for the rapid and automated identification of relevant order parameters involved in the functional transitions of two exemplary cell-signaling proteins central to human disease states.

Local-order metric for condensed-phase environments

NASA Astrophysics Data System (ADS)

Martelli, Fausto; Ko, Hsin-Yu; Oǧuz, Erdal C.; Car, Roberto

2018-02-01

We introduce a local order metric (LOM) that measures the degree of order in the neighborhood of an atomic or molecular site in a condensed medium. The LOM maximizes the overlap between the spatial distribution of sites belonging to that neighborhood and the corresponding distribution in a suitable reference system. The LOM takes a value tending to zero for completely disordered environments and tending to one for environments that perfectly match the reference. The site-averaged LOM and its standard deviation define two scalar order parameters, S and δ S , that characterize with excellent resolution crystals, liquids, and amorphous materials. We show with molecular dynamics simulations that S , δ S , and the LOM provide very insightful information in the study of structural transformations, such as those occurring when ice spontaneously nucleates from supercooled water or when a supercooled water sample becomes amorphous upon progressive cooling.

Insights into the interaction of methotrexate and human serum albumin: A spectroscopic and molecular modeling approach.

PubMed

Cheng, Li-Yang; Fang, Min; Bai, Ai-Min; Ouyang, Yu; Hu, Yan-Jun

2017-08-01

In this study, fluorescence spectroscopy and molecular modeling approaches were employed to investigate the binding of methotrexate to human serum albumin (HSA) under physiological conditions. From the mechanism, it was demonstrated that fluorescence quenching of HSA by methotrexate results from the formation of a methotrexate/HSA complex. Binding parameters calculated using the Stern-Volmer method and the Scatchard method showed that methotrexate binds to HSA with binding affinities in the order 10 4  L·mol -1 . Thermodynamic parameter studies revealed that the binding reaction is spontaneous, and that hydrogen bonds and van der Waals interactions play a major role in the reaction. Site marker competitive displacement experiments and a molecular modeling approach demonstrated that methotrexate binds with appropriate affinity to site I (subdomain IIA) of HSA. Furthermore, we discuss some factors that influence methotrexate binding to HSA. Copyright © 2017 John Wiley & Sons, Ltd.

Comparison of fate profiles of PAHs in soil, sediments and mangrove leaves after oil spills by QSAR and QSPR.

PubMed

Tansel, Berrin; Lee, Mengshan; Tansel, Derya Z

2013-08-15

First order removal rates for 15 polyaromatic hydrocarbons (PAHs) in soil, sediments and mangrove leaves were compared in relation to the parameters used in fate transport analyses (i.e., octanol-water partition coefficient, organic carbon-water partition coefficient, solubility, diffusivity in water, HOMO-LUMO gap, molecular size, molecular aspect ratio). The quantitative structure activity relationships (QSAR) and quantitative structure property relationships (QSPR) showed that the rate of disappearance of PAHs is correlated with their diffusivities in water as well as molecular volumes in different media. Strong correlations for the rate of disappearance of PAHs in sediments could not be obtained in relation to most of the parameters evaluated. The analyses showed that the QSAR and QSPR correlations developed for removal rates of PAHs in soils would not be adequate for sediments and plant tissues. Copyright © 2013 Elsevier Ltd. All rights reserved.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Evolution of short range order in Ar: Liquid to glass and solid transitions-A computational study

NASA Astrophysics Data System (ADS)

Shor, Stanislav; Yahel, Eyal; Makov, Guy

2018-04-01

The evolution of the short range order (SRO) as a function of temperature in a Lennard-Jones model liquid with Ar parameters was determined and juxtaposed with thermodynamic and kinetic properties obtained as the liquid was cooled (heated) and transformed between crystalline solid or glassy states and an undercooled liquid. The Lennard-Jones system was studied by non-equilibrium molecular dynamics simulations of large supercells (approximately 20000 atoms) rapidly cooled or heated at selected quenching rates and at constant pressure. The liquid to solid transition was identified by discontinuities in the atomic volume and molar enthalpy; the glass transition temperature range was identified from the temperature dependence of the self-diffusion. The SRO was studied within the quasi-crystalline model (QCM) framework and compared with the Steinhardt bond order parameters. Within the QCM it was found that the SRO evolves from a bcc-like order in the liquid through a bct-like short range order (c/a=1.2) in the supercooled liquid which persists into the glass and finally to a fcc-like ordering in the crystalline solid. The variation of the SRO that results from the QCM compares well with that obtained with Steinhardt's bond order parameters. The hypothesis of icosahedral order in liquids and glasses is not supported by our results.

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

Identification of Absorption, Distribution, Metabolism, and Excretion (ADME) Genes Relevant to Steatosis Using a Gene Expression Approach

EPA Science Inventory

Absorption, distribution, metabolism, and excretion (ADME) impact chemical concentration and activation of molecular initiating events of Adverse Outcome Pathways (AOPs) in cellular, tissue, and organ level targets. In order to better describe ADME parameters and how they modulat...

Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations.

PubMed

Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart

2015-01-22

Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the trajectory into 10 replicas with different starting velocities.

An NMR database for simulations of membrane dynamics.

PubMed

Leftin, Avigdor; Brown, Michael F

2011-03-01

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

PubMed

Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

2009-03-01

We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.

Impact of higher order diagrams on phase equilibrium calculations for small molecules using lattice cluster theory

NASA Astrophysics Data System (ADS)

Zimmermann, Patrick; Walowski, Christoph; Enders, Sabine

2018-03-01

The Lattice Cluster Theory (LCT) provides a powerful tool to predict thermodynamic properties of large molecules (e.g., polymers) of different molecular architectures. When the pure-component parameters of a certain compound have been derived by adjustment to experimental data and the number of atoms is held constant within the molecule so that only the architecture is changed, the LCT is capable of predicting the properties of isomers without further parameter adjustment just based on the incorporation of molecular architecture. Trying to predict the thermodynamic properties of smaller molecules, one might face some challenges, which are addressed in this contribution. After factoring out the mean field term of the partition function, the LCT poses an expression that involves corrections to the mean field depending on molecular architecture, resulting in the free energy formally being expressed as a double series expansion in lattice coordination number z and interaction energy ɛ ˜ . In the process of deriving all contributing sub-structures within a molecule, some parts have been neglected to this point due to the double series expansion being truncated after the order ɛ˜ 2z-2. We consider the neglected parts that are of the order z-3 and reformulate the expression for the free energy within the LCT to achieve a higher predictive capability of the theory when it comes to small isomers and compressible systems. The modified version was successfully applied for phase equilibrium calculations of binary mixtures composed of linear and branched alkanes.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Molecular design and MD simulations of epitaxial superlattice of self-assembling ternary lipid bilayers

NASA Astrophysics Data System (ADS)

Chou, George; Vaughn, Mark; Cheng, K.

2011-10-01

Multicomponent lipid bilayers represent an important model system for studying cell membranes. At present, an ordered multicomponent phospholipid/cholesterol bilayer system involving charged lipid is still not available. Using a lipid superlattice (SL) model, a 13 x 15 x 15 nm^3 ternary phosphatidylcholine/phosphatidylserine/cholesterol bilayer system in water with simultaneous headgroup SL and acyl chain SL at different depths, or epitaxial SL, of the bilayer has been designed with atomistic detail. The arrangements of this epitaxial SL system were optimized by only two molecular parameters, lattice space and rotational angle of the lipids. Using atomistic MD simulations, we demonstrated the stability of the ordered structures for more than 100 ns. A positional restrained system was also used as a control. This system will provide new insights into understanding the nanodomain structures of cell membranes at the molecular level.

Biomolecular Imaging with Coherent Nonlinear Vibrational Microscopy

PubMed Central

Chung, Chao-Yu; Boik, John; Potma, Eric O.

2014-01-01

Optical imaging with spectroscopic vibrational contrast is a label-free solution for visualizing, identifying, and quantifying a wide range of biomolecular compounds in biological materials. Both linear and nonlinear vibrational microscopy techniques derive their imaging contrast from infrared active or Raman allowed molecular transitions, which provide a rich palette for interrogating chemical and structural details of the sample. Yet nonlinear optical methods, which include both second-order sum-frequency generation (SFG) and third-order coherent Raman scattering (CRS) techniques, offer several improved imaging capabilities over their linear precursors. Nonlinear vibrational microscopy features unprecedented vibrational imaging speeds, provides strategies for higher spatial resolution, and gives access to additional molecular parameters. These advances have turned vibrational microscopy into a premier tool for chemically dissecting live cells and tissues. This review discusses the molecular contrast of SFG and CRS microscopy and highlights several of the advanced imaging capabilities that have impacted biological and biomedical research. PMID:23245525

An accurate computational method for an order parameter with a Markov state model constructed using a manifold-learning technique

NASA Astrophysics Data System (ADS)

Ito, Reika; Yoshidome, Takashi

2018-01-01

Markov state models (MSMs) are a powerful approach for analyzing the long-time behaviors of protein motion using molecular dynamics simulation data. However, their quantitative performance with respect to the physical quantities is poor. We believe that this poor performance is caused by the failure to appropriately classify protein conformations into states when constructing MSMs. Herein, we show that the quantitative performance of an order parameter is improved when a manifold-learning technique is employed for the classification in the MSM. The MSM construction using the K-center method, which has been previously used for classification, has a poor quantitative performance.

Extended polarization in 3rd order SCC-DFTB from chemical potential equilization

PubMed Central

Kaminski, Steve; Giese, Timothy J.; Gaus, Michael; York, Darrin M.; Elstner, Marcus

2012-01-01

In this work we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical potential equilization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for NDDO type methods by Giese and York, has been shown to emend minimal basis methods wrt response properties significantly, and has been applied to SCC-DFTB recently. CPE allows to overcome this inherent limitation of minimal basis methods by supplying an additional response density. The systematic underestimation is thereby corrected quantitatively without the need to extend the atomic orbital basis, i.e. without increasing the overall computational cost significantly. Especially the dependency of polarizability as a function of molecular charge state was significantly improved from the CPE extension of DFTB3. The empirical parameters introduced by the CPE approach were optimized for 172 organic molecules in order to match the results from density functional methods (DFT) methods using large basis sets. However, the first order derivatives of molecular polarizabilities, as e.g. required to compute Raman activities, are not improved by the current CPE implementation, i.e. Raman spectra are not improved. PMID:22894819

(13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

PubMed

Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

2015-12-03

Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate.

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage

PubMed Central

Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm−1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis. PMID:29284007

Effects of low molecular sugars on the retrogradation of tapioca starch gels during storage.

PubMed

Zhang, Xiaoyu; Li, Rongfang; Kang, Huaibin; Luo, Denglin; Fan, Jinling; Zhu, Wenxue; Liu, Xinfang; Tong, Qunyi

2017-01-01

The effects of low molecular sugars (sucrose, glucose and trehalose) on the retrogradation of tapioca starch (TS) gels stored at 4°C for different periods were examined with different methods. Decrease in melting enthalpy (ΔHmelt) were obtained through differential scanning calorimetry analysis. Analysis of decrease in crystallization rate constant (k) and increase in semi-crystallization time (τ1/2) results obtained from retrogradation kinetics indicated that low molecular sugars could retard the retrogradation of TS gels and further revealed trehalose as the best inhibitor among the sugars used in this study. Fourier transform infrared (FTIR) analysis indicated that the intensity ratio of 1047 to 1022 cm-1 was increased with the addition of sugars in the order of trehalose > sucrose > glucose. Decrease in hardness parameters and increase in springiness parameters obtained from texture profile analysis (TPA) analysis also indicated that low molecular sugars could retard the retrogradation of TS gels. The results of FTIR and TPA showed a consistent sugar effect on starch retrogradation with those of DSC and retrogradation kinetics analysis.

Amino acids at water-vapor interfaces: surface activity and orientational ordering.

PubMed

Vöhringer-Martinez, Esteban; Toro-Labbé, Alejandro

2010-10-14

The surface activity and orientational ordering of amino acids at water-vapor interfaces were studied with molecular dynamics simulations in combination with thermodynamic integration and umbrella sampling. Asparagine, representing amino acids with polar side chains, displays no surface activity. Tryptophan, in contrast, with its hydrophobic indole ring as side chain unveils a free energy minimum at the water-vapor interface, which lies 6 kJ/mol under the hydration free energy. To study the orientational ordering of tryptophan along the interface, the order parameter was calculated. At the free energy minimum and at the Gibbs dividing surface, the order parameter reveals a parallel alignment of the indole ring with the water surface exposing the π-system to electrophiles in the hydrophobic phase and indicating polarization dependent spectroscopy. In the vicinity of this position a perpendicular orientation is obtained. The surface excess, calculated from the potential of mean force along the interface, is in excellent agreement with experimental measurements.

Two-order-parameter description of liquid Al under five different pressures

NASA Astrophysics Data System (ADS)

Li, Y. D.; Hao, Qing-Hai; Cao, Qi-Long; Liu, C. S.

2008-11-01

In the present work, using the glue potential, the constant pressure molecular-dynamics simulations of liquid Al under five various pressures and a systematic analysis of the local atomic structures have been performed in order to test the two-order-parameter model proposed by Tanaka [Phys. Rev. Lett. 80, 5750 (1998)] originally for explaining the unusual behaviors of liquid water. The temperature dependence of the bond order parameter Q6 in liquid Al under five different pressures can be well fitted by the functional expression (Q6)/(1-Q6)=Q60exp((ΔE-PΔV)/(kBT)) which produces the energy gain ΔE and the volume change upon the formation of a locally favored structure: ΔE=0.025eV and ΔV=-0.27(Å)3 . ΔE is nearly equal to the difference between the average bond energy of the other type I bonds and the average bond energy of 1551 bonds (characterizing the icosahedronlike local structure); ΔV could be explained as the average volume occupied by one atom in icosahedra minus that occupied by one atom in other structures. With the obtained ΔE and ΔV , it is satisfactorily explained that the density of liquid Al displays a much weaker nonlinear dependence on temperature under lower pressures. So it is demonstrated that the behavior of liquid Al can be well described by the two-order-parameter model.

Molecular Order and Mesophase Investigation of Thiophene-Based Forked Mesogens.

PubMed

Reddy, K Rajasekhar; Lobo, Nitin P; Narasimhaswamy, T

2016-07-14

Thiophene-based rodlike molecules constructed from a three phenyl ring core and terminal dialkoxy chains recognized as forked mesogens are synthesized, and their mesophase properties as well as the molecular order are investigated. The synthesized forked mesogens would serve as model compounds for tetracatenar or biforked mesogens. On the basis of the position of the thiophene link with the rest of the core, 2-substituted and 3-substituted mesogens are realized in which the length of the terminal alkoxy chains is varied. The mesophase properties are evaluated using a hot-stage polarizing microscope and differential scanning calorimetry. For both homologues, the appearance of either nematic phase alone or in conjunction with smectic C phase is noticed depending on the length of the terminal alkoxy chains. The existence of layer ordering characteristic of the smectic C phase is confirmed for a representative mesogen using variable-temperature powder X-ray diffraction. High-resolution solid-state (13)C NMR measurements of C12 homologues of the two series reveal orientational order parameters of all rings of the core as well as terminal chains in the liquid crystalline phase. For both homologues, because of the asymmetry of ring I, the order parameter value is higher in contrast to ring II, ring III, and the thiophene ring. The chemical shifts and (13)C-(1)H dipolar couplings of OCH2 carbons of the terminal dodecyloxy chains provide contrasting conformations, reflecting the orientational constraints. Furthermore, the investigations also reveal that the mesophase range and the tendency for layer ordering are higher for 3-substituted mesogens compared to 2-substituted homologues.

Theoretical study of high-order harmonic generation from the hydrogen molecular ion with a dichromatic spatially inhomogeneous field

NASA Astrophysics Data System (ADS)

Xu, Xiao-Hu; Wang, Yan-Jun; Miao, Xiang-Yang

2018-05-01

We theoretically investigate the enhancement of high-order harmonic generation by numerically solving the non-Born-Oppenheimer time-dependent Schrödinger equation from the hydrogen molecular ion in a dichromatic inhomogeneous laser field. An ultrabroad supercontinuum up to 300 orders spectral width is generated. It is found that not only the inhomogeneity, but also the dichromatic field contributes to the significant extension of the harmonic cutoff compared with a monochromatic inhomogeneous laser field. Meanwhile, the long quantum paths can be suppressed and short ones can be enhanced by selecting optimized inhomogeneous parameter β, intensity and carrier envelope phase of the dichromatic inhomogeneous laser field. Furthermore, by superposing a properly selected range of the harmonic spectrum in the continuum region, an isolated 29-as pulse is generated. Both the classical theory and quantum time-frequency analysis are adopted to explain the physical mechanism.

Combining PALM and SOFI for quantitative imaging of focal adhesions in living cells

NASA Astrophysics Data System (ADS)

Deschout, Hendrik; Lukes, Tomas; Sharipov, Azat; Feletti, Lely; Lasser, Theo; Radenovic, Aleksandra

2017-02-01

Focal adhesions are complicated assemblies of hundreds of proteins that allow cells to sense their extracellular matrix and adhere to it. Although most focal adhesion proteins have been identified, their spatial organization in living cells remains challenging to observe. Photo-activated localization microscopy (PALM) is an interesting technique for this purpose, especially since it allows estimation of molecular parameters such as the number of fluorophores. However, focal adhesions are dynamic entities, requiring a temporal resolution below one minute, which is difficult to achieve with PALM. In order to address this problem, we merged PALM with super-resolution optical fluctuation imaging (SOFI) by applying both techniques to the same data. Since SOFI tolerates an overlap of single molecule images, it can improve the temporal resolution compared to PALM. Moreover, an adaptation called balanced SOFI (bSOFI) allows estimation of molecular parameters, such as the fluorophore density. We therefore performed simulations in order to assess PALM and SOFI for quantitative imaging of dynamic structures. We demonstrated the potential of our PALM-SOFI concept as a quantitative imaging framework by investigating moving focal adhesions in living cells.

Modelling of Cosmic Molecular Masers: Introduction to a Computation Cookbook

NASA Astrophysics Data System (ADS)

Sobolev, Andrej M.; Gray, Malcolm D.

2012-07-01

Numerical modeling of molecular masers is necessary in order to understand their nature and diagnostic capabilities. Model construction requires elaboration of a basic description which allows computation, that is a definition of the parameter space and basic physical relations. Usually, this requires additional thorough studies that can consist of the following stages/parts: relevant molecular spectroscopy and collisional rate coefficients; conditions in and around the masing region (that part of space where population inversion is realized); geometry and size of the masing region (including the question of whether maser spots are discrete clumps or line-of-sight correlations in a much bigger region) and propagation of maser radiation. Output of the maser computer modeling can have the following forms: exploration of parameter space (where do inversions appear in particular maser transitions and their combinations, which parameter values describe a `typical' source, and so on); modeling of individual sources (line flux ratios, spectra, images and their variability); analysis of the pumping mechanism; predictions (new maser transitions, correlations in variability of different maser transitions, and the like). Described schemes (constituents and hierarchy) of the model input and output are based mainly on the experience of the authors and make no claim to be dogmatic.

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

Sucrose in Aqueous Solution Revisited: 2. Adaptively Biased Molecular Dynamics Simulations and Computational Analysis of NMR Relaxation

PubMed Central

Xia, Junchao; Case, David A.

2012-01-01

We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4 M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R1) and transverse (R2) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S2) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80–90% of the conformations having φ – ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures. PMID:22058066

Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

NASA Astrophysics Data System (ADS)

Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

2013-12-01

The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order streams had higher abundances of Sphingomonadaceae spp. and Nordella spp. (both Alphaproteobacteria). The cyanobacteria Chamaesiphon spp. was observed in highest abundance in the first and second order streams of the rock biofilm samples and the cyanobacteria Oscillatoria spp. was in highest abundance in the third order streams. Stream water samples from all orders had high lignin/tannin content and were enriched with carboxylic-rich alicyclic molecules (CRAM). There was an observable shift in in the molecular weight and relative abundance of the CRAM molecules with the CRAM molecules becoming less abundant and having lower molecular weight following the downstream gradient. Multivariate statistical analyses correlated the longitudinal patterns of changes in bacterial community structure to the DOM molecular structure and geochemical parameters across the river continuum.

Isobaric molecular dynamics version of the generalized replica exchange method (gREM): Liquid–vapor equilibrium

DOE PAGES

Malolepsza, Edyta; Secor, Maxim; Keyes, Tom

2015-09-23

A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.

Fundamental Limits:. Developing New Tools for a Better Understanding of Second-Order Molecular Nonlinear Optics

NASA Astrophysics Data System (ADS)

Pérez-Moreno, Javier; Clays, Koen

The generalized Thomas-Kuhn sum rules are used to characterize the nonlinear optical response of organic chromophores in terms of fundamental parameters that can be measured experimentally. The nonlinear optical performance of organic molecules is evaluated from the combination of hyper-Rayleigh scattering measurements and the analysis in terms of the fundamental limits. Different strategies for the enhancement of nonlinear optical behavior at the molecular and supramolecular level are evaluated and new paradigms for the design of more efficient nonlinear optical molecules are proposed and investigated.

Free energy landscape and molecular pathways of gas hydrate nucleation.

PubMed

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

A 17 GHz molecular rectifier

PubMed Central

Trasobares, J.; Vuillaume, D.; Théron, D.; Clément, N.

2016-01-01

Molecular electronics originally proposed that small molecules sandwiched between electrodes would accomplish electronic functions and enable ultimate scaling to be reached. However, so far, functional molecular devices have only been demonstrated at low frequency. Here, we demonstrate molecular diodes operating up to 17.8 GHz. Direct current and radio frequency (RF) properties were simultaneously measured on a large array of molecular junctions composed of gold nanocrystal electrodes, ferrocenyl undecanethiol molecules and the tip of an interferometric scanning microwave microscope. The present nanometre-scale molecular diodes offer a current density increase by several orders of magnitude compared with that of micrometre-scale molecular diodes, allowing RF operation. The measured S11 parameters show a diode rectification ratio of 12 dB which is linked to the rectification behaviour of the direct current conductance. From the RF measurements, we extrapolate a cut-off frequency of 520 GHz. A comparison with the silicon RF-Schottky diodes, architecture suggests that the RF-molecular diodes are extremely attractive for scaling and high-frequency operation. PMID:27694833

Fundamental data on the desorption of pure interstellar ices

NASA Astrophysics Data System (ADS)

Brown, Wendy A.; Bolina, Amandeep S.

2007-01-01

The desorption of molecular ices from grain surfaces is important in a number of astrophysical environments including dense molecular clouds, cometary nuclei and the surfaces and atmospheres of some planets. With this in mind, we have performed a detailed investigation of the desorption of pure water, pure methanol and pure ammonia ices from a model dust-grain surface. We have used these results to determine the desorption energy, order of desorption and the pre-exponential factor for the desorption of these molecular ices from our model surface. We find good agreement between our desorption energies and those determined previously; however, our values for the desorption orders, and hence also the pre-exponential factors, are different to those reported previously. The kinetic parameters derived from our data have been used to model desorption on time-scales relevant to astrophysical processes and to calculate molecular residence times, given in terms of population half-life as a function of temperature. These results show the importance of laboratory data for the understanding of astronomical situations whereby icy mantles are warmed by nearby stars and by other dynamical events.

Correlated ab initio calculations of spectroscopic parameters of SnO within the framework of the higher-order generalized Douglas-Kroll transformation.

PubMed

Wolf, Alexander; Reiher, Markus; Hess, Bernd Artur

2004-05-08

The first molecular calculations with the generalized Douglas-Kroll method up to fifth order in the external potential (DKH5) are presented. We study the spectroscopic parameters and electron affinity of the tin oxide molecule SnO and its anion SnO(-) applying nonrelativistic as well as relativistic calculations with higher orders of the DK approximation. In order to guarantee highly accurate results close to the basis set limit, an all-electron basis for Sn of at least quintuple-zeta quality has been constructed and optimized. All-electron CCSD(T) calculations of the potential energy curves of both SnO and SnO(-) reproduce the experimental values very well. Relative energies and valence properties are already well described with the established standard second-order approximation DKH2 and the higher-order corrections DKH3-DKH5 hardly affect these quantities. However, an accurate description of total energies and inner-shell properties requires superior relativistic schemes up to DKH5. (c) 2004 American Institute of Physics.

Predicting the Plate Dent Test Output in Order to Assess the Performance of Condensed High Explosives

NASA Astrophysics Data System (ADS)

Frem, Dany

2017-01-01

In the present study, a relationship is proposed that is capable of predicting the output of the plate dent test. It is shown that the initial density ?; condensed phase heat of formation ?; the number of carbon (C), nitrogen (N), oxygen (O); and the composition molecular weight (MW) are the most important parameters needed in order to accurately predict the absolute dent depth ? produced on 1018 cold-rolled steel by a detonating organic explosive. The estimated ? values can be used to predict the detonation pressure (P) of high explosives; furthermore, we show that a correlation exists between ? and the Gurney velocity ? parameter. The new correlation is used to accurately estimate ? for several C-H-N-O explosive compositions.

Tracing molecular dephasing in biological tissue

NASA Astrophysics Data System (ADS)

Mokim, M.; Carruba, C.; Ganikhanov, F.

2017-10-01

We demonstrate the quantitative spectroscopic characterization and imaging of biological tissue using coherent time-domain microscopy with a femtosecond resolution. We identify tissue constituents and perform dephasing time (T2) measurements of characteristic Raman active vibrations. This was shown in subcutaneous mouse fat embedded within collagen rich areas of the dermis and the muscle connective tissue. The demonstrated equivalent spectral resolution (<0.3 cm-1) is an order of magnitude better compared to commonly used frequency-domain methods for characterization of biological media. This provides with the important dimensions and parameters in biological media characterization and can become an effective tool in detecting minute changes in the bio-molecular composition and environment that is critical for molecular level diagnosis.

Evaluating Force-Field London Dispersion Coefficients Using the Exchange-Hole Dipole Moment Model.

PubMed

Mohebifar, Mohamad; Johnson, Erin R; Rowley, Christopher N

2017-12-12

London dispersion interactions play an integral role in materials science and biophysics. Force fields for atomistic molecular simulations typically represent dispersion interactions by the 12-6 Lennard-Jones potential using empirically determined parameters. These parameters are generally underdetermined, and there is no straightforward way to test if they are physically realistic. Alternatively, the exchange-hole dipole moment (XDM) model from density-functional theory predicts atomic and molecular London dispersion coefficients from first principles, providing an innovative strategy to validate the dispersion terms of molecular-mechanical force fields. In this work, the XDM model was used to obtain the London dispersion coefficients of 88 organic molecules relevant to biochemistry and pharmaceutical chemistry and the values compared with those derived from the Lennard-Jones parameters of the CGenFF, GAFF, OPLS, and Drude polarizable force fields. The molecular dispersion coefficients for the CGenFF, GAFF, and OPLS models are systematically higher than the XDM-calculated values by a factor of roughly 1.5, likely due to neglect of higher order dispersion terms and premature truncation of the dispersion-energy summation. The XDM dispersion coefficients span a large range for some molecular-mechanical atom types, suggesting an unrecognized source of error in force-field models, which assume that atoms of the same type have the same dispersion interactions. Agreement with the XDM dispersion coefficients is even poorer for the Drude polarizable force field. Popular water models were also examined, and TIP3P was found to have dispersion coefficients similar to the experimental and XDM references, although other models employ anomalously high values. Finally, XDM-derived dispersion coefficients were used to parametrize molecular-mechanical force fields for five liquids-benzene, toluene, cyclohexane, n-pentane, and n-hexane-which resulted in improved accuracy in the computed enthalpies of vaporization despite only having to evaluate a much smaller section of the parameter space.

Magnetohydrodynamic Simulations of a Plunging Black Hole into a Molecular Cloud

NASA Astrophysics Data System (ADS)

Nomura, Mariko; Oka, Tomoharu; Yamada, Masaya; Takekawa, Shunya; Ohsuga, Ken; Takahashi, Hiroyuki R.; Asahina, Yuta

2018-05-01

Using two-dimensional magnetohydrodynamic simulations, we investigated the gas dynamics around a black hole (BH) plunging into a molecular cloud. In these calculations, we assumed a parallel-magnetic-field layer in the cloud. The size of the accelerated region is far larger than the Bondi–Hoyle–Lyttleton radius, being approximately inversely proportional to the Alfvén Mach number for the plunging BH. Our results successfully reproduce the “Y” shape in position–velocity maps of the “Bullet” in the W44 molecular cloud. The size of the Bullet is also reproduced within an order of magnitude using a reasonable parameter set. This consistency supports the shooting model of the Bullet, according to which an isolated BH plunged into a molecular cloud to form a compact broad-velocity-width feature.

Growth of thin films of dicyanovinylanisole on quartz and teflon-coated quartz by physical vapor transport

NASA Technical Reports Server (NTRS)

Pearson, Earl F.

1994-01-01

Organic compounds offer the possibility of molecular engineering in order to optimize the nonlinearity and minimize damage due to the high-power lasers used in nonlinear optical devices. Recently dicyanovinylanisole (DIVA), ((2-methoxyphenyl) methylenepropanedinitrile) has been shown to have a second order nonlinearity 40 times that of alpha-quartz. Debe et. al. have shown that a high degree of orientational order exists for thin films of phthalocyanine grown by physical vapor transport in microgravity. The microgravity environment eliminates convective flow and was critical to the formation of highly ordered dense continuous films in these samples. This work seeks to discover the parameters necessary for the production of thin continuous films of high optical quality in Earth gravity. These parameters must be known before the experiment can be planned for growing DIVA in a microgravity environment. The microgravity grown films are expected to be denser and of better optical quality than the unit gravity films as was observed in the phthalocyanine films.

Influence of polymer network parameters of tragacanth gum-based pH responsive hydrogels on drug delivery.

PubMed

Singh, Baljit; Sharma, Vikrant

2014-01-30

The present article deals with design of tragacanth gum-based pH responsive hydrogel drug delivery systems. The characterization of hydrogels has been carried out by SEMs, EDAX, FTIR, (13)C NMR, XRD, TGA/DTA/DTG and swelling studies. The correlation between reaction conditions and structural parameters of polymer networks such as polymer volume fraction in the swollen state (ϕ), Flory-Huggins interaction parameter (χ), molecular weight of the polymer chain between two neighboring cross links (M¯c), crosslink density (ρ) and mesh size (ξ) has been determined. The different kinetic models such as zero order, first order, Higuchi square root law, Korsmeyer-Peppas model and Hixson-Crowell cube root model were applied and it has been observed that release profile of amoxicillin best followed the first order model for the release of drug from the polymer matrix. The swelling of the hydrogels and release of drug from the drug loaded hydrogels occurred through non-Fickian diffusion mechanism in pH 7.4 solution. Copyright © 2013 Elsevier Ltd. All rights reserved.

Binding affinity toward human prion protein of some anti-prion compounds - Assessment based on QSAR modeling, molecular docking and non-parametric ranking.

PubMed

Kovačević, Strahinja; Karadžić, Milica; Podunavac-Kuzmanović, Sanja; Jevrić, Lidija

2018-01-01

The present study is based on the quantitative structure-activity relationship (QSAR) analysis of binding affinity toward human prion protein (huPrP C ) of quinacrine, pyridine dicarbonitrile, diphenylthiazole and diphenyloxazole analogs applying different linear and non-linear chemometric regression techniques, including univariate linear regression, multiple linear regression, partial least squares regression and artificial neural networks. The QSAR analysis distinguished molecular lipophilicity as an important factor that contributes to the binding affinity. Principal component analysis was used in order to reveal similarities or dissimilarities among the studied compounds. The analysis of in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) parameters was conducted. The ranking of the studied analogs on the basis of their ADMET parameters was done applying the sum of ranking differences, as a relatively new chemometric method. The main aim of the study was to reveal the most important molecular features whose changes lead to the changes in the binding affinities of the studied compounds. Another point of view on the binding affinity of the most promising analogs was established by application of molecular docking analysis. The results of the molecular docking were proven to be in agreement with the experimental outcome. Copyright © 2017 Elsevier B.V. All rights reserved.

Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems.

PubMed

Pérez-Hernández, Guillermo; Noé, Frank

2016-12-13

Analysis of molecular dynamics, for example using Markov models, often requires the identification of order parameters that are good indicators of the rare events, i.e. good reaction coordinates. Recently, it has been shown that the time-lagged independent component analysis (TICA) finds the linear combinations of input coordinates that optimally represent the slow kinetic modes and may serve in order to define reaction coordinates between the metastable states of the molecular system. A limitation of the method is that both computing time and memory requirements scale with the square of the number of input features. For large protein systems, this exacerbates the use of extensive feature sets such as the distances between all pairs of residues or even heavy atoms. Here we derive a hierarchical TICA (hTICA) method that approximates the full TICA solution by a hierarchical, divide-and-conquer calculation. By using hTICA on distances between heavy atoms we identify previously unknown relaxation processes in the bovine pancreatic trypsin inhibitor.

Optimizing Multiple Analyte Injections in Surface Plasmon Resonance Biosensors with Analytes having Different Refractive Index Increments

PubMed Central

Mehand, Massinissa Si; Srinivasan, Bala; De Crescenzo, Gregory

2015-01-01

Surface plasmon resonance-based biosensors have been successfully applied to the study of the interactions between macromolecules and small molecular weight compounds. In an effort to increase the throughput of these SPR-based experiments, we have already proposed to inject multiple compounds simultaneously over the same surface. When specifically applied to small molecular weight compounds, such a strategy would however require prior knowledge of the refractive index increment of each compound in order to correctly interpret the recorded signal. An additional experiment is typically required to obtain this information. In this manuscript, we show that through the introduction of an additional global parameter corresponding to the ratio of the saturating signals associated with each molecule, the kinetic parameters could be identified with similar confidence intervals without any other experimentation. PMID:26515024

Examination of the nature of lattice matched III V semiconductor interfaces using computer simulated molecular beam epitaxial growth I. AC/BC interfaces

NASA Astrophysics Data System (ADS)

Thomsen, M.; Ghaisas, S. V.; Madhukar, A.

1987-07-01

A previously developed computer simulation of molecular beam epitaxial growth of III-V semiconductors based on the configuration dependent reactive incorporation (CDRI) model is extended to allow for two different cation species. Attention is focussed on examining the nature of interfaces formed in lattice matched quantum well structures of the form AC/BC/AC(100). We consider cation species with substantially different effective diffusion lengths, as is the case with Al and Ga during the growth of their respective As compounds. The degree of intermixing occuring at the interface is seen to be dependent upon, among other growth parameters, the pressure of the group V species during growth. Examination of an intraplanar order parameter at the interfaces reveals the existence of short range clustering of the cation species.

Spectroradiometric calibration of the Thematic Mapper and Multispectral Scanner system

NASA Technical Reports Server (NTRS)

Palmer, J. M.; Slater, P. N. (Principal Investigator)

1985-01-01

The effects of the atmosphere on propagating radiation must be known in order to calibrate an in orbit sensor using ground based measurements. A set of model atmosphere parameters, applicable to the White Sands (New Mexico) area is defined with particular attention given to those parameters which are required as input to the Herman Code. The radial size distribution, refractive index, vertical distribution, and visibility of aerosols are discussed as well as the molecular absorbers in the visible and near IR wavelength which produce strong absorption lines. Solar irradiance is also considered.

Molecular Origin of the Self-Assembly of Lanreotide into Nanotubes: A Mutational Approach☆

PubMed Central

Valéry, Céline; Pouget, Emilie; Pandit, Anjali; Verbavatz, Jean-Marc; Bordes, Luc; Boisdé, Isabelle; Cherif-Cheikh, Roland; Artzner, Franck; Paternostre, Maité

2008-01-01

Lanreotide, a synthetic, therapeutic octapeptide analog of somatostatin, self-assembles in water into perfectly hollow and monodisperse (24-nm wide) nanotubes. Lanreotide is a cyclic octapeptide that contains three aromatic residues. The molecular packing of the peptide in the walls of a nanotube has recently been characterized, indicating four hierarchical levels of organization. This is a fascinating example of spontaneous self-organization, very similar to the formation of the gas vesicle walls of Halobacterium halobium. However, this unique peptide self-assembly raises important questions about its molecular origin. We adopted a directed mutation approach to determine the molecular parameters driving the formation of such a remarkable peptide architecture. We have modified the conformation by opening the cycle and by changing the conformation of a Lys residue, and we have also mutated the aromatic side chains of the peptide. We show that three parameters are essential for the formation of lanreotide nanotubes: i), the specificity of two of the three aromatic side chains, ii), the spatial arrangement of the hydrophilic and hydrophobic residues, and iii), the aromatic side chain in the β-turn of the molecule. When these molecular characteristics are modified, either the peptides lose their self-assembling capability or they form less-ordered architectures, such as amyloid fibers and curved lamellae. Thus we have determined key elements of the molecular origins of lanreotide nanotube formation. PMID:17993497

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

Golubev, A.; Balashov, Y.; Mavrin, S.

Washout coefficient Λ is widely used as a parameter in washout models. These models describes overall HTO washout with rain by a first-order kinetic equation, while washout coefficient Λ depends on the type of rain event and rain intensity and empirical parameters a, b. The washout coefficient is a macroscopic parameter and we have considered in this paper its relationship with a microscopic rate K of HTO isotopic exchange in atmospheric humidity and drops of rainwater. We have shown that the empirical parameters a, b can be represented through the rain event characteristics using the relationships of molecular impact rate,more » rain intensity and specific rain water content while washout coefficient Λ can be represented through the exchange rate K, rain intensity, raindrop diameter and terminal raindrop velocity.« less

In Silico Study of Chromatographic Lipophilicity Parameters of 3-(4-Substituted Benzyl)-5-Phenylhydantoins.

PubMed

Sekulic, Tatjana Djakovic; Keleman, Svetlana; Tot, Kristina; Tot, Jadranka; Trisovic, Nemanja; Uscumlic, Gordana

2016-01-01

New synthesized compounds, particularly those with biological activity, are potential drug candidates. This article describes experimental studies performed to estimate lipophilicity parameters of new 3-(4-substituted benzyl)-5-phenylhydantoins. Lipophilicity, as one of the most important molecular characteristics for the activity, was determined using the reversed-phase liquid chromatography (RP-18 stationary phase and methanol-water mobile phase). Molecular structures were used to generate in silico data which were used to estimate pharmacokinetic properties of the investigated compounds. The results show that generally, the investigated compounds attain good bioavailability properties. A more detailed analysis shows that the presence of a nitro, methoxy and tert-butyl group in the molecule is indicated as unfavorable for the oral bioavailability of hydantoins. Multivariate exploratory analysis was used in order to visualize grouping patterns among molecular descriptors as well as among the investigated compounds. Molecular docking study performed for two hydantoins with the highest bioavailability scores shows high binding affinity to tyrosine kinase receptor IGF-1R. The results achieved can be useful as a template for future development and further derivation or modification to obtain more potent and selective antitumor agents.

Physical properties and scaling relations of molecular clouds: the effect of stellar feedback

NASA Astrophysics Data System (ADS)

Grisdale, Kearn; Agertz, Oscar; Renaud, Florent; Romeo, Alessandro B.

2018-06-01

Using hydrodynamical simulations of entire galactic discs similar to the Milky Way, reaching 4.6{ pc} resolution, we study the origins of observed physical properties of giant molecular clouds (GMCs). We find that efficient stellar feedback is a necessary ingredient in order to develop a realistic interstellar medium (ISM), leading to molecular cloud masses, sizes, velocity dispersions and virial parameters in excellent agreement with Milky Way observations. GMC scaling relations observed in the Milky Way, such as the mass-size (M-R), velocity dispersion-size (σ-R), and the σ-RΣ relations, are reproduced in a feedback driven ISM when observed in projection, with M∝R2.3 and σ∝R0.56. When analysed in 3D, GMC scaling relations steepen significantly, indicating potential limitations of our understanding of molecular cloud 3D structure from observations. Furthermore, we demonstrate how a GMC population's underlying distribution of virial parameters can strongly influence the scatter in derived scaling relations. Finally, we show that GMCs with nearly identical global properties exist in different evolutionary stages, where a majority of clouds being either gravitationally bound or expanding, but with a significant fraction being compressed by external ISM pressure, at all times.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

PubMed

Shirts, Michael R; Klein, Christoph; Swails, Jason M; Yin, Jian; Gilson, Michael K; Mobley, David L; Case, David A; Zhong, Ellen D

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

PubMed Central

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to a better than 0.1% relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb’s constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison. PMID:27787702

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

NASA Astrophysics Data System (ADS)

Shirts, Michael R.; Klein, Christoph; Swails, Jason M.; Yin, Jian; Gilson, Michael K.; Mobley, David L.; Case, David A.; Zhong, Ellen D.

2017-01-01

We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally prepared AMBER input files using a combination of the ParmEd and InterMol conversion programs. We find that the energy calculations for all molecular dynamics engines for this molecular set agree to better than 0.1 % relative absolute energy for all energy components, and in most cases an order of magnitude better, when reasonable choices are made for different cutoff parameters. However, there are some surprising sources of statistically significant differences. Most importantly, different choices of Coulomb's constant between programs are one of the largest sources of discrepancies in energies. We discuss the measures required to get good agreement in the energies for equivalent starting configurations between the simulation programs, and the energy differences that occur when simulations are run with program-specific default simulation parameter values. Finally, we discuss what was required to automate this conversion and comparison.

Challenges in Materials Transformation Modeling for Polyolefins Industry

NASA Astrophysics Data System (ADS)

Lai, Shih-Yaw; Swogger, Kurt W.

2004-06-01

Unlike most published polymer processing and/or forming research, the transformation of polyolefins to fabricated articles often involves non-confined flow or so-called free surface flow (e.g. fiber spinning, blown films, and cast films) in which elongational flow takes place during a fabrication process. Obviously, the characterization and validation of extensional rheological parameters and their use to develop rheological constitutive models are the focus of polyolefins materials transformation research. Unfortunately, there are challenges that remain with limited validation for non-linear, non-isothermal constitutive models for polyolefins. Further complexity arises in the transformation of polyolefins in the elongational flow system as it involves stress-induced crystallization process. The complicated nature of elongational, non-linear rheology and non-isothermal crystallization kinetics make the development of numerical methods very challenging for the polyolefins materials forming modeling. From the product based company standpoint, the challenges of materials transformation research go beyond elongational rheology, crystallization kinetics and its numerical modeling. In order to make models useful for the polyolefin industry, it is critical to develop links between molecular parameters to both equipment and materials forming parameters. The recent advances in the constrained geometry catalysis and materials sciences understanding (INSITE technology and molecular design capability) has made industrial polyolefinic materials forming modeling more viable due to the fact that the molecular structure of the polymer can be well predicted and controlled during the polymerization. In this paper, we will discuss inter-relationship (models) among molecular parameters such as polymer molecular weight (Mw), molecular weight distribution (MWD), long chain branching (LCB), short chain branching (SCB or comonomer types and distribution) and their affects on shear and elongational rheologies, on tie-molecules probabilities, on non-isothermal stress-induced crystallization, on crystalline/amorphous orientation vs. mechanical property relationship, etc. All of the above mentioned inter-relationships (models) are critical to the successful development of a knowledge based industrial model. Dow Polyolefins and Elastomers business is one of the world largest polyolefins resin producers with the most advanced INSITE technology and a "6-Day model" molecular design capability. Dow also offers one of the broadest polyolefinic product ranges and applications to the market.

Helium Atom Scattering from C2H6, F2HCCH3, F3CCH2F and C2F6 in Crossed Molecular Beams

NASA Astrophysics Data System (ADS)

Hammer, Markus; Seidel, Wolfhart

1997-10-01

Rotationally unresolved differential cross sections were measured in crossed molecular beam experiments by scattering Helium atoms from Ethane, 1,1-Difluoroethane, 1,1,1,2-Tetrafluoroethane and Hexafluoroethane. The damping of observed diffraction oscillations was used to extract anisotropic interaction potentials for these scattering systems applying the infinite order sudden approximation (IOSA). Binary macroscopic parameters such as second heterogeneous virial coefficients and the coefficients of diffusion and viscosity were computed from these potentials and compared to results from macroscopic experiments.

A molecular theory of smectic C liquid crystals made of rod-like molecules.

PubMed

Govind, A S; Madhusudana, N V

2002-10-01

Organic compounds exhibiting the smectic C phase are made of rod-like molecules that have dipolar groups with lateral components. We argue that the off-axis character of the lateral dipolar groups can account for tilt in layered smectics (SmC, SmC*, SmI etc.). We develop a mean-field theory of the smectic C phase based on a single-particle potential of the form UC is proportional to sin(2theta) cos phi, consistent with the biaxial nature of the phase, where theta and phi are the polar and azimuthal angles, respectively. The hard-rod interactions that favour the smectic A phase with zero tilt angle are also included. The theoretical phase diagrams compare favourably with experimental trends. Our theory also leads to the following results: i) a first-order smectic C to smectic A transition above some value of the McMillan parameter alpha, leading to a tricritical point on the smectic C to smectic A transition line and ii) a first-order smectic C to smectic C transition over a very small range of values of the model parameters. We have also extended the theory to include the next higher-order term in the tilting potential and to include the effect of different tilt angles for the molecular core and the chain in the SmC phase.

Exploring the free energy surface using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-01

Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

Formulation and Evaluation of Tramadol hydrochloride Rectal Suppositories.

PubMed

Saleem, M A; Taher, M; Sanaullah, S; Najmuddin, M; Ali, Javed; Humaira, S; Roshan, S

2008-09-01

Rectal suppositories of tramadol hydrochloride were prepared using different bases and polymers like PEG, cocoa butter, agar and the effect of different additives on in vitro release of tramadol hydrochloride was studied. The agar-based suppositories were non-disintegrating/non-dissolving, whereas PEGs were disintegrating/dissolving and cocoa butter were melting suppositories. All the prepared suppositories were evaluated for various physical parameters like weight variation, drug content and hardness. The PEG and cocoa butter suppositories were evaluated for macromelting range, disintegration and liquefaction time. In vitro release study was performed by USP type I apparatus. The prepared suppositories were within the permissible range of all physical parameters. In vitro drug release was in the order of PEG>Agar>cocoa butter. Addition of PVP, HPMC in agar suppositories retards the release. The mechanism of drug release was diffusion controlled and follows first order kinetics. The results suggested that blends of PEG of low molecular weight (1000) with high molecular weight (4000 and 6000) in different percentage and agar in 10% w/w as base used to formulate rapid release suppositories. The sustained release suppositories can be prepared by addition of PVP, HPMC in agar-based suppositories and by use of cocoa butter as base.

Molecular order and functional properties of starches from three waxy wheat varieties grown in China.

PubMed

Wang, Shujun; Wang, Jinrong; Zhang, Wei; Li, Caili; Yu, Jinglin; Wang, Shuo

2015-08-15

Molecular order and functional properties of starch from three waxy wheat varieties grown in China were investigated by a combination of various technical analyses. The total starch content of the waxy wheat ranged between 54.1% and 55.0%, and the amylose content of the starch was between 0.71% and 1.63%. Average particle diameter of the three starches varied between 16.5 and 17.4 μm. Three waxy wheat starches presented the typical A-type X-ray diffraction pattern, with relative crystallinity between 38.7% and 40.0%. No significant differences were observed in relative crystallinity, IR ratios of 1047/1022 cm(-1) and 1022/995 cm(-1), and FWHH of the band at 480 cm(-1), indicating the similarity in long-range order of crystallites and short-range order of double helices of three starch granules. Small differences were observed in swelling power, gelatinization parameters, pasting viscosities, and in vitro enzymatic digestibility of three waxy wheat starches. Under the stored condition, no retrogradation occurred for three waxy wheat starches. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantitative kinetic theory of active matter

NASA Astrophysics Data System (ADS)

Ihle, Thomas; Chou, Yen-Liang

2014-03-01

Models of self-driven agents similar to the Vicsek model [Phys. Rev. Lett. 75 (1995) 1226] are studied by means of kinetic theory. In these models, particles try to align their travel directions with the average direction of their neighbours. At strong alignment a globally ordered state of collective motion forms. An Enskog-like kinetic theory is derived from the exact Chapman-Kolmogorov equation in phase space using Boltzmann's mean-field approximation of molecular chaos. The kinetic equation is solved numerically by a nonlocal Lattice-Boltzmann-like algorithm. Steep soliton-like waves are observed that lead to an abrupt jump of the global order parameter if the noise level is changed. The shape of the wave is shown to follow a novel scaling law and to quantitatively agree within 3 % with agent-based simulations at large particle speeds. This provides a mean-field mechanism to change the second-order character of the flocking transition to first order. Diagrammatic techniques are used to investigate small particle speeds, where the mean-field assumption of Molecular Chaos is invalid and where correlation effects need to be included.

Application of bi-Helmholtz nonlocal elasticity and molecular simulations to the dynamical response of carbon nanotubes

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

Koutsoumaris, C. Chr.; Tsamasphyros, G. J.; Vogiatzis, G. G.

2015-12-31

The nonlocal theory of elasticity is employed for the study of the free vibrations of carbon nanotubes (CNT). For the first time, a bi-Helmholtz operator has been used instead of the standard Helmholtz operator in a nonlocal beam model. Alongside the continuum formulation and its numerical solution, atomistic Molecular Dynamics (MD) simulations have been conducted in order to directly evaluate the eigenfrequencies of vibrating CNTs with a minimum of adjustable parameters. Our results show that the bi-Helmholtz operator is the most appropriate one to fit MD simulation results. However, the estimation of vibration eigenfrequencies from molecular simulations still remains anmore » open (albeit well-posed) problem.« less

Prediction of stream volatilization coefficients

USGS Publications Warehouse

Rathbun, Ronald E.

1990-01-01

Equations are developed for predicting the liquid-film and gas-film reference-substance parameters for quantifying volatilization of organic solutes from streams. Molecular weight and molecular-diffusion coefficients of the solute are used as correlating parameters. Equations for predicting molecular-diffusion coefficients of organic solutes in water and air are developed, with molecular weight and molal volume as parameters. Mean absolute errors of prediction for diffusion coefficients in water are 9.97% for the molecular-weight equation, 6.45% for the molal-volume equation. The mean absolute error for the diffusion coefficient in air is 5.79% for the molal-volume equation. Molecular weight is not a satisfactory correlating parameter for diffusion in air because two equations are necessary to describe the values in the data set. The best predictive equation for the liquid-film reference-substance parameter has a mean absolute error of 5.74%, with molal volume as the correlating parameter. The best equation for the gas-film parameter has a mean absolute error of 7.80%, with molecular weight as the correlating parameter.

Excitation Spectra and Brightness Optimization of Two-Photon Excited Probes

PubMed Central

Mütze, Jörg; Iyer, Vijay; Macklin, John J.; Colonell, Jennifer; Karsh, Bill; Petrášek, Zdeněk; Schwille, Petra; Looger, Loren L.; Lavis, Luke D.; Harris, Timothy D.

2012-01-01

Two-photon probe excitation data are commonly presented as absorption cross section or molecular brightness (the detected fluorescence rate per molecule). We report two-photon molecular brightness spectra for a diverse set of organic and genetically encoded probes with an automated spectroscopic system based on fluorescence correlation spectroscopy. The two-photon action cross section can be extracted from molecular brightness measurements at low excitation intensities, while peak molecular brightness (the maximum molecular brightness with increasing excitation intensity) is measured at higher intensities at which probe photophysical effects become significant. The spectral shape of these two parameters was similar across all dye families tested. Peak molecular brightness spectra, which can be obtained rapidly and with reduced experimental complexity, can thus serve as a first-order approximation to cross-section spectra in determining optimal wavelengths for two-photon excitation, while providing additional information pertaining to probe photostability. The data shown should assist in probe choice and experimental design for multiphoton microscopy studies. Further, we show that, by the addition of a passive pulse splitter, nonlinear bleaching can be reduced—resulting in an enhancement of the fluorescence signal in fluorescence correlation spectroscopy by a factor of two. This increase in fluorescence signal, together with the observed resemblance of action cross section and peak brightness spectra, suggests higher-order photobleaching pathways for two-photon excitation. PMID:22385865

Crystal water dynamics of guanosine dihydrate: analysis of atomic displacement parameters, time profile of hydrogen-bonding probability, and translocation of water by MD simulation.

PubMed

Yoneda, Shigetaka; Sugawara, Yoko; Urabe, Hisako

2005-01-27

The dynamics of crystal water molecules of guanosine dihydrate are investigated in detail by molecular dynamics (MD) simulation. A 2 ns simulation is performed using a periodic boundary box composed of 4 x 5 x 8 crystallographic unit cells and using the particle-mesh Ewald method for calculation of electrostatic energy. The simulated average atomic positions and atomic displacement parameters are remarkably coincident with the experimental values determined by X-ray analysis, confirming the high accuracy of this simulation. The dynamics of crystal water are analyzed in terms of atomic displacement parameters, orientation vectors, order parameters, self-correlation functions of the orientation vectors, time profiles of hydrogen-bonding probability, and translocations. The simulation clarifies that the average structure is composed of various stable and transient structures of the molecules. The simulated guanosine crystal forms a layered structure, with four water sites per asymmetric unit, classified as either interlayer water or intralayer water. From a detailed analysis of the translocations of water molecules in the simulation, columns of intralayer water molecules along the c axis appear to represent a pathway for hydration and dehydration by a kind of molecular valve mechanism.

Relationship of In Vivo MR Parameters to Histopathological and Molecular Characteristics of Newly Diagnosed, Nonenhancing Lower-Grade Gliomas.

PubMed

Luks, Tracy L; McKnight, Tracy Richmond; Jalbert, Llewellyn E; Williams, Aurelia; Neill, Evan; Lobo, Khadjia A; Persson, Anders I; Perry, Arie; Phillips, Joanna J; Molinaro, Annette M; Chang, Susan M; Nelson, Sarah J

2018-06-05

The goal of this research was to elucidate the relationship between WHO 2016 molecular classifications of newly diagnosed, nonenhancing lower grade gliomas (LrGG), tissue sample histopathology, and magnetic resonance (MR) parameters derived from diffusion, perfusion, and 1 H spectroscopic imaging from the tissue sample locations and the entire tumor. A total of 135 patients were scanned prior to initial surgery, with tumor cellularity scores obtained from 88 image-guided tissue samples. MR parameters were obtained from corresponding sample locations, and histograms of normalized MR parameters within the T2 fluid-attenuated inversion recovery lesion were analyzed in order to evaluate differences between subgroups. For tissue samples, higher tumor scores were related to increased normalized apparent diffusion coefficient (nADC), lower fractional anisotropy (nFA), lower cerebral blood volume (nCBV), higher choline (nCho), and lower N-acetylaspartate (nNAA). Within the T2 lesion, higher tumor grade was associated with higher nADC, lower nFA, and higher Cho to NAA index. Pathological analysis confirmed that diffusion and metabolic parameters increased and perfusion decreased with tumor cellularity. This information can be used to select targets for tissue sampling and to aid in making decisions about treating residual disease. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Simulation of meso-damage of refractory based on cohesion model and molecular dynamics method

NASA Astrophysics Data System (ADS)

Zhao, Jiuling; Shang, Hehao; Zhu, Zhaojun; Zhang, Guoxing; Duan, Leiguang; Sun, Xinya

2018-06-01

In order to describe the meso-damage of the refractories more accurately, and to study of the relationship between the mesostructured of the refractories and the macro-mechanics, this paper takes the magnesia-carbon refractories as the research object and uses the molecular dynamics method to instead the traditional sequential algorithm to establish the meso-particles filling model including small and large particles. Finally, the finite element software-ABAQUS is used to conducts numerical simulation on the meso-damage evolution process of refractory materials. From the results, the process of initiation and propagation of microscopic interface cracks can be observed intuitively, and the macroscopic stress-strain curve of the refractory material is obtained. The results show that the combination of molecular dynamics modeling and the use of Python in the interface to insert the cohesive element numerical simulation, obtaining of more accurate interface parameters through parameter inversion, can be more accurate to observe the interface of the meso-damage evolution process and effective to consider the effect of the mesostructured of the refractory material on its macroscopic mechanical properties.

Multiscale modeling of dislocation-precipitate interactions in Fe: From molecular dynamics to discrete dislocations.

PubMed

Lehtinen, Arttu; Granberg, Fredric; Laurson, Lasse; Nordlund, Kai; Alava, Mikko J

2016-01-01

The stress-driven motion of dislocations in crystalline solids, and thus the ensuing plastic deformation process, is greatly influenced by the presence or absence of various pointlike defects such as precipitates or solute atoms. These defects act as obstacles for dislocation motion and hence affect the mechanical properties of the material. Here we combine molecular dynamics studies with three-dimensional discrete dislocation dynamics simulations in order to model the interaction between different kinds of precipitates and a 1/2〈111〉{110} edge dislocation in BCC iron. We have implemented immobile spherical precipitates into the ParaDis discrete dislocation dynamics code, with the dislocations interacting with the precipitates via a Gaussian potential, generating a normal force acting on the dislocation segments. The parameters used in the discrete dislocation dynamics simulations for the precipitate potential, the dislocation mobility, shear modulus, and dislocation core energy are obtained from molecular dynamics simulations. We compare the critical stresses needed to unpin the dislocation from the precipitate in molecular dynamics and discrete dislocation dynamics simulations in order to fit the two methods together and discuss the variety of the relevant pinning and depinning mechanisms.

Dielectric response of molecules in empirical tight-binding theory

NASA Astrophysics Data System (ADS)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Glass Formation of n-Butanol: Coarse-grained Molecular Dynamics Simulations Using Gay-Berne Potential Model

NASA Astrophysics Data System (ADS)

Xie, Gui-long; Zhang, Yong-hong; Huang, Shi-ping

2012-04-01

Using coarse-grained molecular dynamics simulations based on Gay-Berne potential model, we have simulated the cooling process of liquid n-butanol. A new set of GB parameters are obtained by fitting the results of density functional theory calculations. The simulations are carried out in the range of 290-50 K with temperature decrements of 10 K. The cooling characteristics are determined on the basis of the variations of the density, the potential energy and orientational order parameter with temperature, whose slopes all show discontinuity. Both the radial distribution function curves and the second-rank orientational correlation function curves exhibit splitting in the second peak. Using the discontinuous change of these thermodynamic and structure properties, we obtain the glass transition at an estimate of temperature Tg=120±10 K, which is in good agreement with experimental results 110±1 K.

Evaluation of neutron thermalization parameters and benchmark reactor calculations using a synthetic scattering function for molecular gases

NASA Astrophysics Data System (ADS)

Gillette, V. H.; Patiño, N. E.; Granada, J. R.; Mayer, R. E.

1989-08-01

Using a synthetic incoherent scattering function which describes the interaction of neutrons with molecular gases we provide analytical expressions for zero- and first-order scattering kernels, σ0( E0 → E), σ1( E0 → E), and total cross section σ0( E0). Based on these quantities, we have performed calculations of thermalization parameters and transport coefficients for H 2O, D 2O, C 6H 6 and (CH 2) n at room temperature. Comparison of such values with available experimental data and other calculations is satisfactory. We also generated nuclear data libraries for H 2O with 47 thermal groups at 300 K and performed some benchmark calculations ( 235U, 239Pu, PWR cell and typical APWR cell); the resulting reactivities are compared with experimental data and ENDF/B-IV calculations.

Model of an asymmetric DPPC/DPPS membrane: effect of asymmetry on the lipid properties. A molecular dynamics simulation study.

PubMed

López Cascales, J J; Otero, T F; Smith, Bradley D; González, Carlos; Márquez, M

2006-02-09

The study of asymmetric lipid bilayers is of a crucial importance due to the great number of biological process in which they are involved such as exocytosis, intracellular fusion processes, phospholipid-protein interactions, and signal transduction pathway. In addition, the loss of this asymmetry is a hallmark of the early stages of apoptosis. In this regard, a model of an asymmetric lipid bilayer composed of DPPC and DPPS was simulated by molecular dynamics simulation. Thus, the asymmetric membrane was modeled by 264 lipids, of which 48 corresponded to DPPS- randomly distributed in the same leaflet with 96 DPPC. In the other leaflet, 120 DPPC were placed without DPPS-. Due to the presence of a net charge of -1 for the DPPS- in physiological conditions, 48 Na+ were introduced into the system to balance the charge. To ascertain whether the presence of the DPPS- in only one of the two leaflets perturbs the properties of the DPPC in the other leaflet composed only of DPPC, different properties were studied, such as the atomic density of the different components across the membrane, the electrostatic potential across the membrane, the translational diffusion of DPPC and DPPS, the deuterium order parameters, lipid hydration, and lipid-lipid charge bridges. Thus, we obtained that certain properties such as the surface area lipid molecule, lipid head orientation, order parameter, translational diffusion coefficient, or lipid hydration of DPPC in the leaflet without DPPS remain unperturbed by the presence of DPPS in the other leaflet, compared with a DPPC bilayer. On the other hand, in the leaflet containing DPPS, some of the DPPC properties were strongly affected by the presence of DPPS such as the order parameter or electrostatic potential.

Stereoisomeric effects on dynamic viscosity versus pressure and temperature for the system cis- + trans-decalin

NASA Astrophysics Data System (ADS)

Miyake, Yasufumi; Boned, Christian; Baylaucq, Antoine; Bessières, David; Zéberg-Mikkelsen, Claus K.; Galliéro, Guillaume; Ushiki, Hideharu

2007-07-01

In order to study the influence of stereoisomeric effects on the dynamic viscosity, an extensive experimental study of the viscosity of the binary system composed of the two stereoisomeric molecular forms of decalin - cis and trans - has been carried out for five different mixtures at three temperatures (303.15, 323.15 and 343.15) K and six isobars up to 100 MPa with a falling-body viscometer (a total of 90 points). The experimental relative uncertainty is estimated to be 2%. The variations of dynamic viscosity versus composition are discussed with respect to their behavior due to stereoisomerism. Four different models with a physical and theoretical background are studied in order to investigate how they take the stereoisomeric effect into account through their required model parameters. The evaluated models are based on the hard-sphere scheme, the concepts of the free-volume and the friction theory, and a model derived from molecular dynamics. Overall, a satisfactory representation of the viscosity of this binary system is found for the different models within the considered ( T, p) range taken into account their simplicity. All the models are able to distinguish between the two stereoisomeric decalin compounds. Further, based on the analysis of the model parameters performed on the pure compounds, it has been found that the use of simple mixing rules without introducing any binary interaction parameters are sufficient in order to predict the viscosity of cis + trans-decalin mixtures with the same accuracy in comparison with the experimental values as obtained for the pure compounds. In addition to these models, a semi-empirical self-referencing model and the simple mixing laws of Grunberg-Nissan and Katti-Chaudhri are also applied in the representation of the viscosity behavior of these systems.

Proline puckering parameters for collagen structure simulations

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

Wu, Di, E-mail: diwu@fudan.edu.cn

Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion—proline puckering—becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations.more » Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations.« less

Automated bond order assignment as an optimization problem.

PubMed

Dehof, Anna Katharina; Rurainski, Alexander; Bui, Quang Bao Anh; Böcker, Sebastian; Lenhof, Hans-Peter; Hildebrandt, Andreas

2011-03-01

Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach. We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods. The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.

Effect of thermal treatment on potato starch evidenced by EPR, XRD and molecular weight distribution.

PubMed

Bidzińska, Ewa; Michalec, Marek; Pawcenis, Dominika

2015-12-01

Effect of heating of the potato starch on damages of its structure was investigated by quantitative electron paramagnetic resonance (EPR) spectroscopy, X-ray diffraction and determination of the molecular weight distribution. The measurements were performed in the temperature range commonly used for starch modifications optimizing properties important for industrial applications. Upon thermal treatment, because of breaking of the polymer chains, diminishing of the average molecular weights occurred, which significantly influences generation of radicals, evidenced by EPR. For the relatively mild conditions, with heating parameters not exceeding temperature 230 °C and time of heating equal to 30 min a moderate changes of both the number of thermally generated radicals and the mean molecular weight of the starch were observed. After more drastic thermal treatment (e.g. 2 h at 230 °C), a rapid increase in the radical amount occurred, which was accompanied by significant reduction of the starch molecular size and crystallinity. Experimentally established threshold values of heating parameters should not be exceeded in order to avoid excessive damages of the starch structure accompanied by the formation of the redundant amount of radicals. This requirement is important for industrial applications, because significant destruction of the starch matrix might annihilate the positive influence of the previously performed intentional starch modification. Copyright © 2015 John Wiley & Sons, Ltd.

Molecular weight dependent charge carrier mobility in poly(3,3' '-dioctyl-2,2':5',2' '-terthiophene).

PubMed

Verilhac, Jean-Marie; Pokrop, Rafal; LeBlevennec, Gilles; Kulszewicz-Bajer, Irena; Buga, Katarzyna; Zagorska, Malgorzata; Sadki, Said; Pron, Adam

2006-07-13

Poly(3,3' '-dioctyl-2,2':5',2' '-terthiophene), a polymer recently used for the fabrication of organic field effect transistors, has been fractionated into five fractions distinctly differing in their molecular weights (Mn), with the goal of determining the influence of the degree of polymerization (DPn) on its principal physicochemical parameters. It has been demonstrated that within the Mn range studied (from 1.5 kDa to 10.5 kDa by SEC), corresponding to DPn from 10 to 38, the polymer band gap steadily decreases with growing molecular weight, which is clearly manifested by an increasing bathochromic shift of the band originating from the pi-pi* transition. The same trend is observed for the HOMO level, determined from the onset of the p-doping in cyclic voltammetry, which shifts from -5.10 eV to -4.90 eV for the lowest and the highest molecular weight fractions, respectively. The most pronounced influence of DPn has been found for the charge carriers' mobility-one of the most important parameters of field effect transistors (FETs) fabricated from this polymer. A fourfold increase in DPn results in an increase of the carriers' mobility by more than 3 orders of magnitude. Comparison of these results with those obtained for fractionated regioregular poly(3-hexylthiophene) shows a strikingly similar behavior of both polymers with respect to the molecular weight.

Bayesian estimation of realized stochastic volatility model by Hybrid Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Takaishi, Tetsuya

2014-03-01

The hybrid Monte Carlo algorithm (HMCA) is applied for Bayesian parameter estimation of the realized stochastic volatility (RSV) model. Using the 2nd order minimum norm integrator (2MNI) for the molecular dynamics (MD) simulation in the HMCA, we find that the 2MNI is more efficient than the conventional leapfrog integrator. We also find that the autocorrelation time of the volatility variables sampled by the HMCA is very short. Thus it is concluded that the HMCA with the 2MNI is an efficient algorithm for parameter estimations of the RSV model.

The Dense Gas Fraction in the Central Molecular Zone in the Milky Way

NASA Astrophysics Data System (ADS)

Vargas-Salazar, Irene; Battersby, Cara; Walker, Daniel; Zhang, Qizhou; CMZoom

2017-01-01

The Central Molecular Zone (CMZ), a large reservoir of dense molecular gas occupying the central 500pc of the Milky Way, is an extreme star-formation environment where the validity of star formation prescriptions can be tested. The star formation rate (SFR) in the CMZ is about an order of magnitude lower than predicted by the currently accepted prescriptions. An international team lead by PIs Battersby and Keto conducted a survey from 2013-2016 called CMZoom using the Submillimeter Array (SMA) to characterize star formation within resolved molecular clouds in this extreme region. One of the main goals of this survey is to further quantify and understand the low SFR found in this region of the Galaxy. Here, we use the CASA software package to run synthetic observations of hydrodynamical simulations of molecular clouds and vary the observation parameters in such a way that we explore the real parameter space that was probed during the survey. The purpose of this is to investigate how the different observational parameters affect the resultant data. Afterwards, we estimate the “dense gas fraction” (DGF) found in regions across the CMZ. This estimate was found by using the interferometric flux from SMA and the single-dish flux from the Bolocam Galactic Plane Survey. We analyzed the effects that different locations of the CMZ had on these approximate DGF. With these simulations and DGF estimates, we are able to generate improved methods to analyze the data from this survey that will help understand star formation in an extreme environment.The SAO REU program is funded in part by the National Science Foundation REU and Department of Defense ASSURE programs under NSF Grant no.1262851, and by the Smithsonian Institution.

Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing.

PubMed

Chen, Bor-Sen; Hsu, Chih-Yuan

2012-10-26

Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular communication. Synchronization of a population of synthetic genetic oscillators is an important design in practical applications, because such a population distributed over different host cells needs to exploit molecular phenomena simultaneously in order to emerge a biological phenomenon. However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. Therefore, robust synchronization is an important design topic in nonlinear stochastic coupled synthetic genetic oscillators with intrinsic kinetic parameter fluctuations and extrinsic molecular noise. Initially, the condition for robust synchronization of synthetic genetic oscillators was derived based on Hamilton Jacobi inequality (HJI). We found that if the synchronization robustness can confer enough intrinsic robustness to tolerate intrinsic parameter fluctuation and extrinsic robustness to filter the environmental noise, then robust synchronization of coupled synthetic genetic oscillators is guaranteed. If the synchronization robustness of a population of nonlinear stochastic coupled synthetic genetic oscillators distributed over different host cells could not be maintained, then robust synchronization could be enhanced by external control input through quorum sensing molecules. In order to simplify the analysis and design of robust synchronization of nonlinear stochastic synthetic genetic oscillators, the fuzzy interpolation method was employed to interpolate several local linear stochastic coupled systems to approximate the nonlinear stochastic coupled system so that the HJI-based synchronization design problem could be replaced by a simple linear matrix inequality (LMI)-based design problem, which could be solved with the help of LMI toolbox in MATLAB easily. If the synchronization robustness criterion, i.e. the synchronization robustness ≥ intrinsic robustness + extrinsic robustness, then the stochastic coupled synthetic oscillators can be robustly synchronized in spite of intrinsic parameter fluctuation and extrinsic noise. If the synchronization robustness criterion is violated, external control scheme by adding inducer can be designed to improve synchronization robustness of coupled synthetic genetic oscillators. The investigated robust synchronization criteria and proposed external control method are useful for a population of coupled synthetic networks with emergent synchronization behavior, especially for multi-cellular, engineered networks.

Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing

PubMed Central

2012-01-01

Background Collective rhythms of gene regulatory networks have been a subject of considerable interest for biologists and theoreticians, in particular the synchronization of dynamic cells mediated by intercellular communication. Synchronization of a population of synthetic genetic oscillators is an important design in practical applications, because such a population distributed over different host cells needs to exploit molecular phenomena simultaneously in order to emerge a biological phenomenon. However, this synchronization may be corrupted by intrinsic kinetic parameter fluctuations and extrinsic environmental molecular noise. Therefore, robust synchronization is an important design topic in nonlinear stochastic coupled synthetic genetic oscillators with intrinsic kinetic parameter fluctuations and extrinsic molecular noise. Results Initially, the condition for robust synchronization of synthetic genetic oscillators was derived based on Hamilton Jacobi inequality (HJI). We found that if the synchronization robustness can confer enough intrinsic robustness to tolerate intrinsic parameter fluctuation and extrinsic robustness to filter the environmental noise, then robust synchronization of coupled synthetic genetic oscillators is guaranteed. If the synchronization robustness of a population of nonlinear stochastic coupled synthetic genetic oscillators distributed over different host cells could not be maintained, then robust synchronization could be enhanced by external control input through quorum sensing molecules. In order to simplify the analysis and design of robust synchronization of nonlinear stochastic synthetic genetic oscillators, the fuzzy interpolation method was employed to interpolate several local linear stochastic coupled systems to approximate the nonlinear stochastic coupled system so that the HJI-based synchronization design problem could be replaced by a simple linear matrix inequality (LMI)-based design problem, which could be solved with the help of LMI toolbox in MATLAB easily. Conclusion If the synchronization robustness criterion, i.e. the synchronization robustness ≥ intrinsic robustness + extrinsic robustness, then the stochastic coupled synthetic oscillators can be robustly synchronized in spite of intrinsic parameter fluctuation and extrinsic noise. If the synchronization robustness criterion is violated, external control scheme by adding inducer can be designed to improve synchronization robustness of coupled synthetic genetic oscillators. The investigated robust synchronization criteria and proposed external control method are useful for a population of coupled synthetic networks with emergent synchronization behavior, especially for multi-cellular, engineered networks. PMID:23101662

Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal.

PubMed

Neale, Chris; Madill, Chris; Rauscher, Sarah; Pomès, Régis

2013-08-13

All molecular dynamics simulations are susceptible to sampling errors, which degrade the accuracy and precision of observed values. The statistical convergence of simulations containing atomistic lipid bilayers is limited by the slow relaxation of the lipid phase, which can exceed hundreds of nanoseconds. These long conformational autocorrelation times are exacerbated in the presence of charged solutes, which can induce significant distortions of the bilayer structure. Such long relaxation times represent hidden barriers that induce systematic sampling errors in simulations of solute insertion. To identify optimal methods for enhancing sampling efficiency, we quantitatively evaluate convergence rates using generalized ensemble sampling algorithms in calculations of the potential of mean force for the insertion of the ionic side chain analog of arginine in a lipid bilayer. Umbrella sampling (US) is used to restrain solute insertion depth along the bilayer normal, the order parameter commonly used in simulations of molecular solutes in lipid bilayers. When US simulations are modified to conduct random walks along the bilayer normal using a Hamiltonian exchange algorithm, systematic sampling errors are eliminated more rapidly and the rate of statistical convergence of the standard free energy of binding of the solute to the lipid bilayer is increased 3-fold. We compute the ratio of the replica flux transmitted across a defined region of the order parameter to the replica flux that entered that region in Hamiltonian exchange simulations. We show that this quantity, the transmission factor, identifies sampling barriers in degrees of freedom orthogonal to the order parameter. The transmission factor is used to estimate the depth-dependent conformational autocorrelation times of the simulation system, some of which exceed the simulation time, and thereby identify solute insertion depths that are prone to systematic sampling errors and estimate the lower bound of the amount of sampling that is required to resolve these sampling errors. Finally, we extend our simulations and verify that the conformational autocorrelation times estimated by the transmission factor accurately predict correlation times that exceed the simulation time scale-something that, to our knowledge, has never before been achieved.

[Personalized molecular medicine: new paradigms in the treatment of cochlear implant and cancer patients].

PubMed

Zenner, H P; Pfister, M; Friese, N; Zrenner, E; Röcken, M

2014-07-01

To evaluate present options for the indication of cochlear implants (CI) and new forms of treatment for head and neck cancer, melanomas and basal cell carcinomas, with emphasis on future perspectives. A literature search was performed in the PubMed database. Search parameters were "personalized medicine", "individualized medicine" and "molecular medicine". Personalized medicine based on molecular-genetic evaluation of functional proteins such as otoferlin, connexin 26 and KCNQ4 or the Usher gene is becoming increasingly important for the indication of CI in the context of infant deafness. Determination of HER2/EGFR mutations in the epithelial growth factor receptor (EGFR) gene may be an important prognostic parameter for therapeutic decisions in head and neck cancer patients. In basal cell carcinoma therapy, mutations in the Hedgehog (PCTH1) and Smoothened (SMO) pathways strongly influence the indication of therapeutic Hedgehog inhibition, e.g. using small molecules. Analyses of c-Kit receptor, BRAF-600E and NRAS mutations are required for specific molecular therapy of metastasizing melanomas. The significant advances in the field of specific molecular therapy are best illustrated by the availability of the first gene therapeutic procedures for treatment of RPE65-induced infantile retinal degradation. The aim of personalized molecular medicine is to identify patients who will respond particularly positively or negatively (e.g. in terms of adverse side effects) to a therapy using the methods of molecular medicine. This should allow a specific therapy to be successfully applied or preclude its indication in order to avoid serious adverse side effects. This approach serves to stratify patients for adequate treatment.

Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo

PubMed Central

2016-01-01

Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4–7 × 10−12 N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo. These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids. PMID:27534697

Mammalian phospholipid homeostasis: evidence that membrane curvature elastic stress drives homeoviscous adaptation in vivo.

PubMed

Dymond, Marcus K

2016-08-01

Several theories of phospholipid homeostasis have postulated that cells regulate the molecular composition of their bilayer membranes, such that a common biophysical membrane parameter is under homeostatic control. Two commonly cited theories are the intrinsic curvature hypothesis, which states that cells control membrane curvature elastic stress, and the theory of homeoviscous adaptation, which postulates cells control acyl chain packing order (membrane order). In this paper, we present evidence from data-driven modelling studies that these two theories correlate in vivo. We estimate the curvature elastic stress of mammalian cells to be 4-7 × 10(-12) N, a value high enough to suggest that in mammalian cells the preservation of membrane order arises through a mechanism where membrane curvature elastic stress is controlled. These results emerge from analysing the molecular contribution of individual phospholipids to both membrane order and curvature elastic stress in nearly 500 cellular compositionally diverse lipidomes. Our model suggests that the de novo synthesis of lipids is the dominant mechanism by which cells control curvature elastic stress and hence membrane order in vivo These results also suggest that cells can increase membrane curvature elastic stress disproportionately to membrane order by incorporating polyunsaturated fatty acids into lipids. © 2016 The Author(s).

Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory.

PubMed

Tiwari, Ambuj; Ensing, Bernd

2016-12-22

Outer sphere electron transfer between two ions in aqueous solution is a rare event on the time scale of first principles molecular dynamics simulations. We have used transition path sampling to generate an ensemble of reactive trajectories of the self-exchange reaction between a pair of Ru 2+ and Ru 3+ ions in water. To distinguish between the reactant and product states, we use as an order parameter the position of the maximally localised Wannier center associated with the transferring electron. This allows us to align the trajectories with respect to the moment of barrier crossing and compute statistical averages over the path ensemble. We compare our order parameter with two typical reaction coordinates used in applications of Marcus theory of electron transfer: the vertical gap energy and the solvent electrostatic potential at the ions.

Anomalous phase behavior of first-order fluid-liquid phase transition in phosphorus

NASA Astrophysics Data System (ADS)

Zhao, G.; Wang, H.; Hu, D. M.; Ding, M. C.; Zhao, X. G.; Yan, J. L.

2017-11-01

Although the existence of liquid-liquid phase transition has become more and more convincing, whether it will terminate at a critical point and what is the order parameter are still open. To explore these questions, we revisit the fluid-liquid phase transition (FLPT) in phosphorus (P) and study its phase behavior by performing extensive first-principles molecular dynamics simulations. The FLPT observed in experiments is well reproduced, and a fluid-liquid critical point (FLCP) at T = 3000 ˜ 3500 K, P = 1.5-2.0 Kbar is found. With decreasing temperature from the FLCP along the transition line, the density difference (Δρ) between two coexisting phases first increases from zero and then anomalously decreases; however, the entropy difference (ΔS) continuously increases from zero. These features suggest that an order parameter containing contributions from both the density and the entropy is needed to describe the FLPT in P, and at least at low temperatures, the entropy, instead of the density, governs the FLPT.

Nonequilibrium Green's function theory for nonadiabatic effects in quantum electron transport

NASA Astrophysics Data System (ADS)

Kershaw, Vincent F.; Kosov, Daniel S.

2017-12-01

We develop nonequilibrium Green's function-based transport theory, which includes effects of nonadiabatic nuclear motion in the calculation of the electric current in molecular junctions. Our approach is based on the separation of slow and fast time scales in the equations of motion for Green's functions by means of the Wigner representation. Time derivatives with respect to central time serve as a small parameter in the perturbative expansion enabling the computation of nonadiabatic corrections to molecular Green's functions. Consequently, we produce a series of analytic expressions for non-adiabatic electronic Green's functions (up to the second order in the central time derivatives), which depend not solely on the instantaneous molecular geometry but likewise on nuclear velocities and accelerations. An extended formula for electric current is derived which accounts for the non-adiabatic corrections. This theory is concisely illustrated by the calculations on a model molecular junction.

Nonequilibrium Green's function theory for nonadiabatic effects in quantum electron transport.

PubMed

Kershaw, Vincent F; Kosov, Daniel S

2017-12-14

We develop nonequilibrium Green's function-based transport theory, which includes effects of nonadiabatic nuclear motion in the calculation of the electric current in molecular junctions. Our approach is based on the separation of slow and fast time scales in the equations of motion for Green's functions by means of the Wigner representation. Time derivatives with respect to central time serve as a small parameter in the perturbative expansion enabling the computation of nonadiabatic corrections to molecular Green's functions. Consequently, we produce a series of analytic expressions for non-adiabatic electronic Green's functions (up to the second order in the central time derivatives), which depend not solely on the instantaneous molecular geometry but likewise on nuclear velocities and accelerations. An extended formula for electric current is derived which accounts for the non-adiabatic corrections. This theory is concisely illustrated by the calculations on a model molecular junction.

Water nucleation in helium, methane, and argon: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Dumitrescu, Lucia R.; Huinink, Henk; Smeulders, David M. J.; Dam, Jacques A. M.; Gaastra-Nedea, Silvia V.

2018-05-01

Nucleation of highly supersaturated water vapor in helium, methane, and argon carrier gases at 350 K was investigated using molecular dynamics simulations. Nucleation rates obtained from the mean first passage time (MFPT) method are typically one order of magnitude lower than those from the Yasuoka and Matsumoto method, which can be attributed to the overestimation of the critical cluster size in the MFPT method. It was found that faster nucleation will occur in carrier gases that have better thermalization properties such that latent heat is removed more efficiently. These thermalization properties are shown to be strongly dependent on the molecular mass and Lennard-Jones (LJ) parameters. By varying the molecular mass, for unaltered LJ parameters, it was found that a heavier carrier gas removes less heat although it has a higher collision rate with water than a lighter carrier. Thus, it was shown that a clear distinction between water vapor-carrier gas collisions and water cluster-carrier gas collisions is indispensable for understanding the effect of collision rates on thermalization. It was also found that higher concentration of carrier gas leads to higher nucleation rate. The nucleation rates increased by a factor of 1.3 for a doubled concentration and by almost a factor of two for a tripled concentration.

Chemoenzymatic synthesis of new derivatives of glycyrrhetinic acid with antiviral activity. Molecular docking study.

PubMed

Zígolo, M Antonela; Salinas, Maximiliano; Alché, Laura; Baldessari, Alicia; Liñares, Guadalupe García

2018-08-01

We present an efficient approach to the synthesis of a series of glycyrrhetinic acid derivatives. Six derivatives, five of them new compounds, were obtained through chemoenzymatic reactions in very good to excellent yield. In order to find the optimal reaction conditions, the influence of various parameters such as enzyme source, nucleophile:substrate ratio, enzyme:substrate ratio, solvent and temperature was studied. The excellent results obtained by lipase catalysis made the procedure very efficient considering their advantages such as mild reaction conditions and low environmental impact. Moreover, in order to explain the reactivity of glycyrrhetinic acid and the acetylated derivative to different nucleophiles in the enzymatic reactions, molecular docking studies were carried out. In addition, one of the synthesized compounds exhibited remarkable antiviral activity against TK + and TK- strains of Herpes simplex virus type 1 (HSV-1), sensitive and resistant to acyclovir (ACV) treatment. Copyright © 2018 Elsevier Inc. All rights reserved.

On the Utility of the Molecular Oxygen Dayglow Emissions as Proxies for Middle Atmospheric Ozone

NASA Technical Reports Server (NTRS)

Mlynczak, Martin G.; Olander, Daphne S.

1995-01-01

Molecular oxygen dayglow emissions arise in part from processes related to the Hartley band photolysis of ozone. It is therefore possible to derive daytime ozone concentrations from measurements of the volume emission rate of either dayglow. The accuracy to which the ozone concentration can be inferred depends on the accuracy to which numerous kinetic and spectroscopic rate constants are known, including rates which describe the excitation of molecular oxygen by processes that are not related to the ozone concentration. We find that several key rate constants must be known to better than 7 percent accuracy in order to achieve an inferred ozone concentration accurate to 15 percent from measurements of either dayglow. Currently, accuracies for various parameters typically range from 5 to 100 percent.

Molecular Packing of Amiphiphiles with Crown Polar Heads at the Air-Water Interface

NASA Astrophysics Data System (ADS)

Larson, K.; Vaknin, D.; Villavicencio, O.; McGrath, D.; Tsukruk, V. V.

2002-03-01

An amphiphilic compound containing a benzyl-15-crown-5 focal point, azobenzene spacer, and a dodecyl tail as a peripheral group has been investigated at the air-water interface. X-ray grazing incident diffraction and reflectivity were preformed on the Langmuir monolayers to elucidate molecular packing and orientation. At high surface pressure, we observed intralayer packing of the alkyl tails with doubling parameters of the conventional orthorhombic unit cell (supercell) and long-range positional ordering. High tilt of the alkyl tails of about 58º from the surface normal was a signature of molecular packing caused by a large mismatch between the cross-sectional areas of the polar heads and the alkyl tail. Higher generation molecules of the same series display straight tail orientation and hexagonal lateral packing.

Molecular dynamics simulations of stratum corneum lipid models: fatty acids and cholesterol.

PubMed

Höltje, M; Förster, T; Brandt, B; Engels, T; von Rybinski, W; Höltje, H D

2001-03-09

We report the results of an investigation on stratum corneum lipids, which present the main barrier of the skin. Molecular dynamics simulations, thermal analysis and FTIR measurements were applied. The primary objective of this work was to study the effect of cholesterol on skin structure and dynamics. Two molecular models were constructed, a free fatty acid bilayer (stearic acid, palmitic acid) and a fatty acid/cholesterol mixture at a 1:1 molar ratio. Our simulations were performed at constant pressure and temperature on a nanosecond time scale. The resulting model structures were characterized by calculating surface areas per headgroup, conformational properties, atom densities and order parameters of the fatty acids. Analysis of the simulations indicates that the free fatty acid fraction of stratum corneum lipids stays in a highly ordered crystalline state at skin temperatures. The phase behavior is strongly influenced when cholesterol is added. Cholesterol smoothes the rigid phases of the fatty acids: the order of the hydrocarbon tails (mainly of the last eight bonds) is reduced, the area per molecule becomes larger, the fraction of trans dihedrals is lower and the hydrophobic thickness is reduced. The simulation results are in good agreement with our experimental data from FTIR analysis and NIR-FT Raman spectroscopy.

Photoinduced ultrafast charge-order melting: Charge-order inversion and nonthermal effects

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

van Veenendaal, Michel

2016-09-01

The effect of photoexcitation is studied for a system with checkerboard charge order induced by displacements of ligands around a metal site. The motion of the ligands is treated classically and the electronic charges are simplified to two-level molecular bond charges. The calculations are done for a checkerboard charge-ordered system with about 100 000 ligand oscillators coupled to a fixed-temperature bath. The initial photoexcitation is followed by a rapid decrease in the charge-order parameter within 50–100 femtoseconds while leaving the correlation length almost unchanged. Depending on the fluence, a complete melting of the charge order occurs in less than amore » picosecond. While for low fluences, the system returns to its original state, for full melting, it recovers to its broken-symmetry state leading to an inversion of the charge order. For small long-range interactions, recovery can be slow due to domain formation.« less

Photoinduced ultrafast charge-order melting: Charge-order inversion and nonthermal effects

DOE PAGES

van Veenendaal, Michel

2016-09-01

The effect of photoexcitation is studied for a system with checkerboard charge order induced by displacements of ligands around a metal site. The motion of the ligands is treated classically and the electronic charges are simplified to two-level molecular bond charges. The calculations are done for a checkerboard charge-ordered system with about 100 000 ligand oscillators coupled to a fixed-temperature bath. The initial photoexcitation is followed by a rapid decrease in the charge-order parameter within 50–100 femtoseconds while leaving the correlation length almost unchanged. Depending on the fluence, a complete melting of the charge order occurs in less than amore » picosecond. While for low fluences, the system returns to its original state, for full melting, it recovers to its broken-symmetry state leading to an inversion of the charge order. Finally, for small long-range interactions, recovery can be slow due to domain formation.« less

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Observation of the de Vries behavior in SmA* phase of a liquid crystal using polarised Raman scattering and infrared spectroscopy

NASA Astrophysics Data System (ADS)

Kocot, A.; Vij, J. K.; Perova, T. S.; Merkel, K.; Swaminathan, V.; Sreenilayam, S. P.; Yadav, N.; Panov, V. P.; Stevenson, P. J.; Panov, A.; Rodriguez-Lojo, D.

2017-09-01

Two approaches exist in the literature for describing the orientational distribution function (ODF) of the molecular directors in SmA* phase of liquid crystals, though several models are recently proposed in the literature for explaining the de Vries behaviour. These ODFs correspond to either the conventional unimodal arrangements of molecular directors arising from the mean field theory that leads to the broad or sugar-loaf like distribution or to the "diffuse-cone-shaped" type distribution proposed by de Vries. The hypothesis by de Vries provides for a realistic explanation as to how at a molecular level, a first-order SmA* to SmC* transition can occur where the uniform molecular director azimuthal distributions condense to values lying within a narrow range of angles; finally these condense to a single value while at the same time ensuring a little or no concomitant shrinkage in the layer spacing. The azimuthal distribution of the in-layer directors is probed using IR and polarized Raman spectroscopic techniques. The latter allows us to obtain the ODF and the various order parameters for the uniaxial and the biaxial phases. Based on the results of these measurements, we conclude that the "cone-shaped" (or volcano-shaped) de Vries type of distribution can most preferably describe SmA* where "a first-order phase transition from SmA* to SmC*" and a low layer shrinkage can both be easily explained.

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Competition of the connectivity with the local and the global order in polymer melts and crystals

NASA Astrophysics Data System (ADS)

Bernini, S.; Puosi, F.; Barucco, M.; Leporini, D.

2013-11-01

The competition between the connectivity and the local or global order in model fully flexible chain molecules is investigated by molecular-dynamics simulations. States with both missing (melts) and high (crystal) global order are considered. Local order is characterized within the first coordination shell (FCS) of a tagged monomer and found to be lower than in atomic systems in both melt and crystal. The role played by the bonds linking the tagged monomer to FCS monomers (radial bonds), and the bonds linking two FCS monomers (shell bonds) is investigated. The detailed analysis in terms of Steinhardt's orientation order parameters Ql (l = 2 - 10) reveals that increasing the number of shell bonds decreases the FCS order in both melt and crystal. Differently, the FCS arrangements organize the radial bonds. Even if the molecular chains are fully flexible, the distribution of the angle formed by adjacent radial bonds exhibits sharp contributions at the characteristic angles θ ≈ 70°, 122°, 180°. The fractions of adjacent radial bonds with θ ≈ 122°, 180° are enhanced by the global order of the crystal, whereas the fraction with 70° ≲ θ ≲ 110° is nearly unaffected by the crystallization. Kink defects, i.e., large lateral displacements of the chains, are evidenced in the crystalline state.

Molecular Dynamics Simulation of Calbindin D9k in Apo, Singly and Doubly Loaded States in Various Side-Chains

NASA Astrophysics Data System (ADS)

Thapa, Mahendra Bahadur

Calbindin D9k (CAB) is a single domain calcium-binding protein and is the smallest members of the calmodulin superfamily, possessing a pair of calcium-binding EF-hands, and structures for all four states have been determined and extensively characterized experimentally. Because of the tremendous advancement in hardware and software computer technologies in recent years, longer and more realistic molecular dynamics (MD) simulations of a protein are possible now in reasonable periods of time. These advances were exploited to generate multiple, all-atom MD simulations of CAB via the AMBER software package, and the resulting trajectories were employed to calculate backbone order parameters of the apo, the singly and the doubly loaded states of calcium in CAB. The results are in very good agreement with corresponding experimental NMR-based (Nuclear Magnetic Resonance spectroscopy) results, and are improved in comparison to those calculated over a decade ago; use of modified force fields played a key role in the observed improvements. The apo state is the most flexible, and the singly loaded and the doubly loaded states are similar, thus supporting positive cooperativity in line with the experimental results. Further, B-factor calculations of backbone atoms for these calcium-binding states of calbindin D9k also support such cooperativity. Although changes in side-chain motions are not necessarily correlated to changes in protein backbone mobility, past studies on the comparison of experimental and simulated methyl side-chain NMR relaxation parameters of CAB for the doubly-loaded state reported significant improvements in the quantitative representation of side-chain motion by MD simulation. In this project, the order parameters for various side chains in apo, singly loaded and doubly loaded states of CAB were calculated. The primary goal of this work was to determine whether or not the allosteric effect of calcium binding, as observed via the backbone order parameters, also extended to the amino acid side chains, and if so, to what extent. Such information could be useful in better understanding the physical basis of cooperative calcium binding in CAB. Most of the residues which provide ligands to bind calcium at the binding sites support positive cooperativity, as observed when Ca-Cß, Cß-C?, C-C bond and C-O bonds of COO groups of aspartic and glutamic acid residues, the C-N bond of the side-chain amide group in asparagine and glutamine residues, and the N-H bonds of amide (NH2) group order parameters were studied. There are only a few residues containing methyl groups that are involved in providing ligands to the calcium, and the studies of order parameters of C-C bond and C-H bond of these methyl groups did not exhibit the cooperativity effect upon calcium binding; the simulated C-C bond order parameter of the methyl group symmetry axis did correlate well with the experimental results for the fully loaded state of CAB (4ICB). Analysis of the MD trajectories using GSATools and MutInf, provided valuable insights into possible pathways for communicating allosteric effects between the two calcium-binding sites of CAB.

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

PubMed

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

2016-03-21

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

Molecular dynamics simulations of shock waves in hydroxyl-terminated polybutadiene melts: Mechanical and structural responses

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

Fröhlich, Markus G., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu; Sewell, Thomas D., E-mail: SewellT@missouri.edu; Thompson, Donald L., E-mail: FroehlichM@missouri.edu, E-mail: ThompsonDon@missouri.edu

2014-01-14

The mechanical and structural responses of hydroxyl-terminated cis-1,4-polybutadiene melts to shock waves were investigated by means of all-atom non-reactive molecular dynamics simulations. The simulations were performed using the OPLS-AA force field but with the standard 12-6 Lennard-Jones potential replaced by the Buckingham exponential-6 potential to better represent the interactions at high compression. Monodisperse systems containing 64, 128, and 256 backbone carbon atoms were studied. Supported shock waves were generated by impacting the samples onto stationary pistons at impact velocities of 1.0, 1.5, 2.0, and 2.5 km s{sup −1}, yielding shock pressures between approximately 2.8 GPa and 12.5 GPa. Single-molecule structuralmore » properties (squared radii of gyration, asphericity parameters, and orientational order parameters) and mechanical properties (density, shock pressure, shock temperature, and shear stress) were analyzed using a geometric binning scheme to obtain spatio-temporal resolution in the reference frame centered on the shock front. Our results indicate that while shear stress behind the shock front is relieved on a ∼0.5 ps time scale, a shock-induced transition to a glass-like state occurs with a concomitant increase of structural relaxation times by several orders of magnitude.« less

Molecular Dynamics Simulations of Poly(ethylene oxide) Grafted onto Silica Immersed in Melt of Homopolymers.

PubMed

Benková, Zuzana; Cordeiro, M Natália D S

2015-09-22

Tuning of surface properties plays an important role in applications ranging from material engineering to biomedicine/chemistry. The interactions of chains grafted to a solid support and exposed to a matrix of chemically identical chains represent an intriguing issue. In this work, the behavior of poly(ethylene oxide) (PEO) chains grafted irreversibly onto an amorphous silica and immersed in the matrix of free PEO chains of different polymerization degree is studied using molecular dynamics simulations. The density distributions of grafted and free PEO chains, the height of the grafted layer, overlap parameters, and orientation order parameters depend not only on the grafting density but also on the length of free chains which confirm the entropic nature of the interactions between the grafted and free chains. In order to achieve a complete expulsion of the free chains from the grafted layer, a grafting density as high as 3.5 nm(-2) is necessary. Free PEO chains of 9 monomers leave the grafted layer at lower grafting densities than the longer PEO chains of 18 monomers in contrast with the theoretical predictions. The height of the grafted layer evolves with the grafting density in the presence of free chains in qualitative agreement with the theoretical phase diagram.

Kinetic limitation of chemical ordering in Bi2Te3-x Se x layers grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Schreyeck, S.; Brunner, K.; Kirchner, A.; Bass, U.; Grauer, S.; Schumacher, C.; Gould, C.; Karczewski, G.; Geurts, J.; Molenkamp, L. W.

2016-04-01

We study the chemical ordering in Bi2Te3-x Se x grown by molecular beam epitaxy on Si substrates. We produce films in the full composition range from x  =  0 to 3, and determine their material properties using energy dispersive x-ray spectroscopy, x-ray diffraction and Raman spectroscopy. By fitting the parameters of a kinetic growth model to these results, we obtain a consistent description of growth at a microscopic level. Our main finding is that despite the incorporation of Se in the central layer being much more probable than that of Te, the formation of a fully ordered Te-Bi-Se-Bi-Te layer is prevented by kinetic of the growth process. Indeed, the Se concentration in the central layer of Bi2Te2Se1 reaches a maximum of only  ≈75% even under ideal growth conditions. A second finding of our work is that the intensity ratio of the 0 0 12 and 0 0 6 x-ray reflections serves as an experimentally accessible quantitative measure of the degree of ordering in these films.

Clustering pesticides according to their molecular properties and their impacts by considering additional ecotoxicological parameters in the TyPol method

NASA Astrophysics Data System (ADS)

Traore, Harouna; Crouzet, Olivier; Mamy, Laure; Sireyjol, Christine; Rossard, Virginie; Servien, Remy; Latrille, Eric; Benoit, Pierre

2017-04-01

The understanding of the fate of pesticides and their environmental impacts largely relies on their molecular properties. We recently developed 'TyPol' (Typology of Pollutants), a clustering method based on statistical analyses combining several environmental endpoints (i.e. environmental parameters such as sorption coefficient, degradation half-life) and one ecotoxicological one (bioconcentration factor), and structural molecular descriptors (number of atoms in the molecule, molecular surface, dipole moment, energy of orbitals…). TyPol has been conceived on the available knowledge on QSAR of a wide diversity of organic compounds (Mamy et al., 2015). This approach also allows to focus on transformation products present in different clusters and to infer possible changes in environmental fate consecutively to different degradation processes (Servien et al., 2014; Benoit et al., 2016). The initial version of TyPol did not include any ecotoxicological parameters except the bioconcentration factor (BCF), which informs more on the transfer along the trophic chain rather than on the effects on non-target organisms. The objective was to implement the TyPol database with a data set of ecotoxicological data concerning pesticides and several aquatic and terrestrial organisms, in order to test the possibility to extend TyPol to ecotoxicological effects on various organisms. The data analysis (available literature and databases) revealed that relevant ecotoxicological endpoints for terrestrial organisms such as soil microorganisms and macroinvertebrates are lacking compared to aquatic organisms. We have added seven parameters for acute (EC50, LC50) and chronic (NOEC) toxicological effects for the following organisms: Daphnia, Algae, Lemna and Earthworm. In this new configuration, TyPol was used to classify about 45 pesticides in different behavioural and ecotoxicity clusters. The clustering results were analyzed to reveals relationships between molecular descriptors, environmental parameters and the added toxicological parameters. Some trends between soil adsorption or Kow coefficient and the acute toxicity towards earthworms or algae were highlighted, and discussed on the basis of the concept of contaminant bioavailability. This proof-of-concept study also showed that the in silico clustering method TyPol can successfully address new questions and can be expanded with other parameters of interest. Keywords: pesticides, toxicity, QSAR, clustering, PLS References : Servien R., Mamy L., Li Z., Rossard V., Latrille E., Bessac F., Patureau D., Benoit P., 2014. TyPol - A new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior. Chemosphere, 111, 613-622. Mamy L., Patureau D., Barriuso E., Bedos C., Bessac F., Louchart X., Martin-Laurent F., Miege C., Benoit P., 2015. Prediction of the fate of organic compounds in the environment from their molecular properties: A review. Critical Reviews in Environmental Science and Technology, 45, 12, 1277-1377 (Open access). Benoit P., Mamy L., Servien R., Li Z., Latrille E., Rossard V., Bessac F., Patureau D., Martin-Laurent F. 2017. Categorizing chlordecone potential degradation products to explore their environmental fate. Science of the Total Environment, 574, 781-795.

End Groups of Functionalized Siloxane Oligomers Direct Block-Copolymeric or Liquid-Crystalline Self-Assembly Behavior

PubMed Central

2016-01-01

Monodisperse oligodimethylsiloxanes end-functionalized with the hydrogen-bonding ureidopyrimidinone (UPy) motif undergo phase separation between their aromatic end groups and dimethylsiloxane midblocks to form ordered nanostructures with domain spacings of <5 nm. The self-assembly behavior of these well-defined oligomers resembles that of high degree of polymerization (N)–high block interaction parameter (χ) linear diblock copolymers despite their small size. Specifically, the phase morphology varies from lamellar to hexagonal to body-centered cubic with increasing asymmetry in molecular volume fraction. Mixing molecules with different molecular weights to give dispersity >1.13 results in disorder, showing importance of molecular monodispersity for ultrasmall ordered phase separation. In contrast, oligodimethylsiloxanes end-functionalized with an O-benzylated UPy derivative self-assemble into lamellar nanostructures regardless of volume fraction because of the strong preference of the end groups to aggregate in a planar geometry. Thus, these molecules display more classically liquid-crystalline self-assembly behavior where the lamellar bilayer thickness is determined by the siloxane midblock. Here the lamellar nanostructure is tolerant to molecular polydispersity. We show the importance of end groups in high χ–low N block molecules, where block-copolymer-like self-assembly in our UPy-functionalized oligodimethylsiloxanes relies upon the dominance of phase separation effects over directional end group aggregation. PMID:27054381

Structure-property-glass transition relationships in non-isocyanate polyurethanes investigated by dynamic nanoindentation

NASA Astrophysics Data System (ADS)

Weyand, Stephan; Blattmann, Hannes; Schimpf, Vitalij; Mülhaupt, Rolf; Schwaiger, Ruth

2016-07-01

Newly developed green-chemistry approaches towards the synthesis of non-isocyanate polyurethane (NIPU) systems represent a promising alternative to polyurethanes (PU) eliminating the need for harmful ingredients. A series of NIPU systems were studied using different nanoindentation techniques in order to understand the influence of molecular parameters on the mechanical behavior. Nanoindentation revealed a unique characteristic feature of those materials, i.e. stiffening with increasing deformation. It is argued that the origin of this observed stiffening is a consequence of the thermodynamic state of the polymer network, the molecular characteristics of the chemical building blocks and resulting anisotropic elastic response of the network structure. Flat-punch nanoindentation was applied in order to characterize the constitutive viscoelastic nature of the materials. The complex modulus shows distinct changes as a function of the NIPU network topology illustrating the influence of the chemical building blocks. The reproducibility of the data indicates that the materials are homogeneous over the volumes sampled by nanoindentation. Our study demonstrates that nanoindentation is very well-suited to investigate the molecular characteristics of NIPU materials that cannot be quantified in conventional experiments. Moreover, the technique provides insight into the functional significance of complex molecular architectures thereby supporting the development of NIPU materials with tailored properties.

Comparative studies on molecular structure, vibrational spectra and hyperpolarizabilies of NLO chromophore Ethyl 4-Dimethylaminobenzoate

NASA Astrophysics Data System (ADS)

Amalanathan, M.; Jasmine, G. Femina; Roy, S. Dawn Dharma

2017-08-01

The molecular structure, vibrational spectra and polarizabilities of Ethyl 4-Dimethylaminobenzoate (EDAB) was investigated by density functional theory employing Becke's three parameter hybrid exchange functional with Lee-Yang-Parr (B3LYP) co-relational functional involving 6-311++G(d,p) basis set and compared with some other levels. A detailed interpretation of the IR and Raman spectra of EDBA have been reported and analyzed. Complete vibrational assignments of the vibrational modes have been done on the basis of the potential energy distribution (TED) using VEDA software. The molecular electrostatic potential mapped onto total density surface has been obtained. A study on the electronic properties, such as absorption wavelength, and frontier molecular orbitals energy, was performed using DFT approach. The stability of the molecule arising from hyper conjugative interactions and accompanying charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The natural and Mulliken charge also calculated and compared with different level of calculation. The dipole moment, polarizability and first, second order hyperpolarizabilities of the title molecule were calculated and compared with the experimental values. The energy gap between frontier orbitals has been used along with electric moments and first order hyperpolarizability, to understand the non linear optical (NLO) activity of the molecule. The NLO activity of molecule was confirmed by SHG analysis.

An analytical equation of state for describing isotropic-nematic phase equilibria of Lennard-Jones chain fluids with variable degree of molecular flexibility

NASA Astrophysics Data System (ADS)

van Westen, Thijs; Oyarzún, Bernardo; Vlugt, Thijs J. H.; Gross, Joachim

2015-06-01

We develop an equation of state (EoS) for describing isotropic-nematic (IN) phase equilibria of Lennard-Jones (LJ) chain fluids. The EoS is developed by applying a second order Barker-Henderson perturbation theory to a reference fluid of hard chain molecules. The chain molecules consist of tangentially bonded spherical segments and are allowed to be fully flexible, partially flexible (rod-coil), or rigid linear. The hard-chain reference contribution to the EoS is obtained from a Vega-Lago rescaled Onsager theory. For the description of the (attractive) dispersion interactions between molecules, we adopt a segment-segment approach. We show that the perturbation contribution for describing these interactions can be divided into an "isotropic" part, which depends only implicitly on orientational ordering of molecules (through density), and an "anisotropic" part, for which an explicit dependence on orientational ordering is included (through an expansion in the nematic order parameter). The perturbation theory is used to study the effect of chain length, molecular flexibility, and attractive interactions on IN phase equilibria of pure LJ chain fluids. Theoretical results for the IN phase equilibrium of rigid linear LJ 10-mers are compared to results obtained from Monte Carlo simulations in the isobaric-isothermal (NPT) ensemble, and an expanded formulation of the Gibbs-ensemble. Our results show that the anisotropic contribution to the dispersion attractions is irrelevant for LJ chain fluids. Using the isotropic (density-dependent) contribution only (i.e., using a zeroth order expansion of the attractive Helmholtz energy contribution in the nematic order parameter), excellent agreement between theory and simulations is observed. These results suggest that an EoS contribution for describing the attractive part of the dispersion interactions in real LCs can be obtained from conventional theoretical approaches designed for isotropic fluids, such as a Perturbed-Chain Statistical Associating Fluid Theory approach.

Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas.

PubMed

Andoh, Yoshimichi; Aoki, Noriyuki; Okazaki, Susumu

2016-02-28

Molecular dynamics (MD) calculations of lipid bilayers modeling the plasma membranes of normal mouse hepatocytes and hepatomas in water have been performed under physiological isothermal-isobaric conditions (310.15 K and 1 atm). The changes in the membrane properties induced by hepatic canceration were investigated and were compared with previous MD calculations included in our previous study of the changes in membrane properties induced by murine thymic canceration. The calculated model membranes for normal hepatocytes and hepatomas comprised 23 and 24 kinds of lipids, respectively. These included phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. We referred to previously published experimental values for the mole fraction of the lipids adopted in the present calculations. The calculated structural and dynamic properties of the membranes such as lateral structure, order parameters, lateral self-diffusion constants, and rotational correlation times all showed that hepatic canceration causes plasma membranes to become more ordered laterally and less fluid. Interestingly, this finding contrasts with the less ordered structure and increased fluidity of plasma membranes induced by thymic canceration observed in our previous MD study.

Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas

NASA Astrophysics Data System (ADS)

Andoh, Yoshimichi; Aoki, Noriyuki; Okazaki, Susumu

2016-02-01

Molecular dynamics (MD) calculations of lipid bilayers modeling the plasma membranes of normal mouse hepatocytes and hepatomas in water have been performed under physiological isothermal-isobaric conditions (310.15 K and 1 atm). The changes in the membrane properties induced by hepatic canceration were investigated and were compared with previous MD calculations included in our previous study of the changes in membrane properties induced by murine thymic canceration. The calculated model membranes for normal hepatocytes and hepatomas comprised 23 and 24 kinds of lipids, respectively. These included phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, lysophospholipids, and cholesterol. We referred to previously published experimental values for the mole fraction of the lipids adopted in the present calculations. The calculated structural and dynamic properties of the membranes such as lateral structure, order parameters, lateral self-diffusion constants, and rotational correlation times all showed that hepatic canceration causes plasma membranes to become more ordered laterally and less fluid. Interestingly, this finding contrasts with the less ordered structure and increased fluidity of plasma membranes induced by thymic canceration observed in our previous MD study.

The torsional energy profile of 1,2-diphenylethane: an ab initio study

NASA Astrophysics Data System (ADS)

Ivanov, Petko M.

1997-08-01

Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

Combined analysis of whole human blood parameters by Raman spectroscopy and spectral-domain low-coherence interferometry

NASA Astrophysics Data System (ADS)

Gnyba, M.; Wróbel, M. S.; Karpienko, K.; Milewska, D.; Jedrzejewska-Szczerska, M.

2015-07-01

In this article the simultaneous investigation of blood parameters by complementary optical methods, Raman spectroscopy and spectral-domain low-coherence interferometry, is presented. Thus, the mutual relationship between chemical and physical properties may be investigated, because low-coherence interferometry measures optical properties of the investigated object, while Raman spectroscopy gives information about its molecular composition. A series of in-vitro measurements were carried out to assess sufficient accuracy for monitoring of blood parameters. A vast number of blood samples with various hematological parameters, collected from different donors, were measured in order to achieve a statistical significance of results and validation of the methods. Preliminary results indicate the benefits in combination of presented complementary methods and form the basis for development of a multimodal system for rapid and accurate optical determination of selected parameters in whole human blood. Future development of optical systems and multivariate calibration models are planned to extend the number of detected blood parameters and provide a robust quantitative multi-component analysis.

Quantum chemical calculations of Cr2O3/SnO2 using density functional theory method

NASA Astrophysics Data System (ADS)

Jawaher, K. Rackesh; Indirajith, R.; Krishnan, S.; Robert, R.; Das, S. Jerome

2018-03-01

Quantum chemical calculations have been employed to study the molecular effects produced by Cr2O3/SnO2 optimised structure. The theoretical parameters of the transparent conducting metal oxides were calculated using DFT / B3LYP / LANL2DZ method. The optimised bond parameters such as bond lengths, bond angles and dihedral angles were calculated using the same theory. The non-linear optical property of the title compound was calculated using first-order hyperpolarisability calculation. The calculated HOMO-LUMO analysis explains the charge transfer interaction between the molecule. In addition, MEP and Mulliken atomic charges were also calculated and analysed.

Molecular dynamics simulations of classical sound absorption in a monatomic gas

NASA Astrophysics Data System (ADS)

Ayub, M.; Zander, A. C.; Huang, D. M.; Cazzolato, B. S.; Howard, C. Q.

2018-05-01

Sound wave propagation in argon gas is simulated using molecular dynamics (MD) in order to determine the attenuation of acoustic energy due to classical (viscous and thermal) losses at high frequencies. In addition, a method is described to estimate attenuation of acoustic energy using the thermodynamic concept of exergy. The results are compared against standing wave theory and the predictions of the theory of continuum mechanics. Acoustic energy losses are studied by evaluating various attenuation parameters and by comparing the changes in behavior at three different frequencies. This study demonstrates acoustic absorption effects in a gas simulated in a thermostatted molecular simulation and quantifies the classical losses in terms of the sound attenuation constant. The approach can be extended to further understanding of acoustic loss mechanisms in the presence of nanoscale porous materials in the simulation domain.

A new basis set for molecular bending degrees of freedom.

PubMed

Jutier, Laurent

2010-07-21

We present a new basis set as an alternative to Legendre polynomials for the variational treatment of bending vibrational degrees of freedom in order to highly reduce the number of basis functions. This basis set is inspired from the harmonic oscillator eigenfunctions but is defined for a bending angle in the range theta in [0:pi]. The aim is to bring the basis functions closer to the final (ro)vibronic wave functions nature. Our methodology is extended to complicated potential energy surfaces, such as quasilinearity or multiequilibrium geometries, by using several free parameters in the basis functions. These parameters allow several density maxima, linear or not, around which the basis functions will be mainly located. Divergences at linearity in integral computations are resolved as generalized Legendre polynomials. All integral computations required for the evaluation of molecular Hamiltonian matrix elements are given for both discrete variable representation and finite basis representation. Convergence tests for the low energy vibronic states of HCCH(++), HCCH(+), and HCCS are presented.

Comparison of Phase Field Crystal and Molecular Dynamics Simulations for a Shrinking Grain

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

Radhakrishnan, Balasubramaniam; Gorti, Sarma B; Nicholson, Don M

2012-01-01

The Phase-Field Crystal (PFC) model represents the atomic density as a continuous function, whose spatial distribution evolves at diffusional, rather than vibrational time scales. PFC provides a tool to study defect interactions at the atomistic level but over longer time scales than in molecular dynamics (MD). We examine the behavior of the PFC model with the goal of relating the PFC parameters to physical parameters of real systems, derived from MD simulations. For this purpose we model the phenomenon of the shrinking of a spherical grain situated in a matrix. By comparing the rate of shrinking of the central grainmore » using MD and PFC we obtain a relationship between PFC and MD time scales for processes driven by grain boundary diffusion. The morphological changes in the central grain including grain shape and grain rotation are also examined in order to assess the accuracy of the PFC in capturing the evolution path predicted by MD.« less

From boiling point to glass transition temperature: transport coefficients in molecular liquids follow three-parameter scaling.

PubMed

Schmidtke, B; Petzold, N; Kahlau, R; Hofmann, M; Rössler, E A

2012-10-01

The phenomenon of the glass transition is an unresolved problem in condensed matter physics. Its prominent feature, the super-Arrhenius temperature dependence of the transport coefficients, remains a challenge to be described over the full temperature range. For a series of molecular glass formers, we combined τ(T) collected from dielectric spectroscopy and dynamic light scattering covering a range 10(-12) s < τ(T) < 10(2) s. Describing the dynamics in terms of an activation energy E(T), we distinguish a high-temperature regime characterized by an Arrhenius law with a constant activation energy E(∞) and a low-temperature regime for which E(coop)(T) ≡ E(T)-E(∞) increases exponentially while cooling. A scaling is introduced, specifically E(coop)(T)/E(∞) [proportionality] exp[-λ(T/T(A)-1)], where λ is a fragility parameter and T(A) a reference temperature proportional to E(∞). In order to describe τ(T) still the attempt time τ(∞) has to be specified. Thus, a single interaction parameter E(∞) describing the high-temperature regime together with λ controls the temperature dependence of low-temperature cooperative dynamics.

Molecular effective coverage surface area of optical clearing agents for predicting optical clearing potential

NASA Astrophysics Data System (ADS)

Feng, Wei; Ma, Ning; Zhu, Dan

2015-03-01

The improvement of methods for optical clearing agent prediction exerts an important impact on tissue optical clearing technique. The molecular dynamic simulation is one of the most convincing and simplest approaches to predict the optical clearing potential of agents by analyzing the hydrogen bonds, hydrogen bridges and hydrogen bridges type forming between agents and collagen. However, the above analysis methods still suffer from some problem such as analysis of cyclic molecule by reason of molecular conformation. In this study, a molecular effective coverage surface area based on the molecular dynamic simulation was proposed to predict the potential of optical clearing agents. Several typical cyclic molecules, fructose, glucose and chain molecules, sorbitol, xylitol were analyzed by calculating their molecular effective coverage surface area, hydrogen bonds, hydrogen bridges and hydrogen bridges type, respectively. In order to verify this analysis methods, in vitro skin samples optical clearing efficacy were measured after 25 min immersing in the solutions, fructose, glucose, sorbitol and xylitol at concentration of 3.5 M using 1951 USAF resolution test target. The experimental results show accordance with prediction of molecular effective coverage surface area. Further to compare molecular effective coverage surface area with other parameters, it can show that molecular effective coverage surface area has a better performance in predicting OCP of agents.

Relationships between the structure of natural organic matter and its reactivity towards molecular ozone and hydroxyl radicals

USGS Publications Warehouse

Westerhoff, P.; Aiken, G.; Amy, G.; Debroux, J.

1999-01-01

Oxidation reaction rate parameters for molecular ozone (O3) and hydroxyl (HO) radicals with a variety of hydrophobic organic acids (HOAs) isolated from different geographic locations were determined from batch ozonation studies. Rate parameter values, obtained under equivalent dissolved organic carbon concentrations in both the presence and absence of non-NOM HO radical scavengers, varied as a function of NOM structure. First-order rate constants for O3 consumption (k(O3)) averaged 8.8 x 10-3 s-1, ranging from 3.9 x 10-3 s-1 for a groundwater HOA to > 16 x 10-3 s-1 for river HOAs with large terrestrial carbon inputs. The average second-order rate constant (k(HO,DOC) between HO radicals and NOM was 3.6 x 108 l (mol C)-1 s-1; a mass of 12 g C per mole C was used in all calculations. Specific ultraviolet absorbance (SUVA) at 254 or 280 nm of the HOAs correlated well (r > 0.9) with O3 consumption rate parameters, implying that organic ??-electrons strongly and selectively influence oxidative reactivity. HO radical reactions with NOM were less selective, although correlation between k(HO,DOC) and SUVA existed. Other physical-chemical properties of NOM, such as aromatic and aliphatic carbon content from 13C-NMR spectroscopy, proved less sensitive for predicting oxidation reactivity than SUVA. The implication of this study is that the structural nature of NOM varies temporally and spatially in a water source, and both the nature and amount of NOM will influence oxidation rates.

The Effects of Molecular Properties on Ready Biodegradation of Aromatic Compounds in the OECD 301B CO2 Evolution Test.

PubMed

He, Mei; Mei, Cheng-Fang; Sun, Guo-Ping; Li, Hai-Bei; Liu, Lei; Xu, Mei-Ying

2016-07-01

Ready biodegradation is the primary biodegradability of a compound, which is used for discriminating whether a compound could be rapidly and readily biodegraded in the natural ecosystems in a short period and has been applied extensively in the environmental risk assessment of many chemicals. In this study, the effects of 24 molecular properties (including 2 physicochemical parameters, 10 geometrical parameters, 6 topological parameters, and 6 electronic parameters) on the ready biodegradation of 24 kinds of synthetic aromatic compounds were investigated using the OECD 301B CO2 Evolution test. The relationship between molecular properties and ready biodegradation of these aromatic compounds varied with molecular properties. A significant inverse correlation was found for the topological parameter TD, five geometrical parameters (Rad, CAA, CMA, CSEV, and N c), and the physicochemical parameter K ow, and a positive correlation for two topological parameters TC and TVC, whereas no significant correlation was observed for any of the electronic parameters. Based on the correlations between molecular properties and ready biodegradation of these aromatic compounds, the importance of molecular properties was demonstrated as follows: geometrical properties > topological properties > physicochemical properties > electronic properties. Our study first demonstrated the effects of molecular properties on ready biodegradation by a number of experiment data under the same experimental conditions, which should be taken into account to better guide the ready biodegradation tests and understand the mechanisms of the ready biodegradation of aromatic compounds.

Physical re-examination of parameters on a molecular collisions-based diffusion model for diffusivity prediction in polymers.

PubMed

Ohashi, Hidenori; Tamaki, Takanori; Yamaguchi, Takeo

2011-12-29

Molecular collisions, which are the microscopic origin of molecular diffusive motion, are affected by both the molecular surface area and the distance between molecules. Their product can be regarded as the free space around a penetrant molecule defined as the "shell-like free volume" and can be taken as a characteristic of molecular collisions. On the basis of this notion, a new diffusion theory has been developed. The model can predict molecular diffusivity in polymeric systems using only well-defined single-component parameters of molecular volume, molecular surface area, free volume, and pre-exponential factors. By consideration of the physical description of the model, the actual body moved and which neighbor molecules are collided with are the volume and the surface area of the penetrant molecular core. In the present study, a semiempirical quantum chemical calculation was used to calculate both of these parameters. The model and the newly developed parameters offer fairly good predictive ability. © 2011 American Chemical Society

Effects of Different PER Translational Kinetics on the Dynamics of a Core Circadian Clock Model

PubMed Central

Nieto, Paula S.; Revelli, Jorge A.; Garbarino-Pico, Eduardo; Condat, Carlos A.; Guido, Mario E.; Tamarit, Francisco A.

2015-01-01

Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis. PMID:25607544

Effects of different per translational kinetics on the dynamics of a core circadian clock model.

PubMed

Nieto, Paula S; Revelli, Jorge A; Garbarino-Pico, Eduardo; Condat, Carlos A; Guido, Mario E; Tamarit, Francisco A

2015-01-01

Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.

A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

PubMed

Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

2015-04-14

One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions.

Revealing chemophoric sites in organophosphorus insecticides through the MIA-QSPR modeling of soil sorption data.

PubMed

Daré, Joyce K; Silva, Cristina F; Freitas, Matheus P

2017-10-01

Soil sorption of insecticides employed in agriculture is an important parameter to probe the environmental fate of organic chemicals. Therefore, methods for the prediction of soil sorption of new agrochemical candidates, as well as for the rationalization of the molecular characteristics responsible for a given sorption profile, are extremely beneficial for the environment. A quantitative structure-property relationship method based on chemical structure images as molecular descriptors provided a reliable model for the soil sorption prediction of 24 widely used organophosphorus insecticides. By means of contour maps obtained from the partial least squares regression coefficients and the variable importance in projection scores, key molecular moieties were targeted for possible structural modification, in order to obtain novel and more environmentally friendly insecticide candidates. The image-based descriptors applied encode molecular arrangement, atoms connectivity, groups size, and polarity; consequently, the findings in this work cannot be achieved by a simple relationship with hydrophobicity, usually described by the octanol-water partition coefficient. Copyright © 2017 Elsevier Inc. All rights reserved.

Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-05-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

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

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Combined Yamamoto approach for simultaneous estimation of adsorption isotherm and kinetic parameters in ion-exchange chromatography.

PubMed

Rüdt, Matthias; Gillet, Florian; Heege, Stefanie; Hitzler, Julian; Kalbfuss, Bernd; Guélat, Bertrand

2015-09-25

Application of model-based design is appealing to support the development of protein chromatography in the biopharmaceutical industry. However, the required efforts for parameter estimation are frequently perceived as time-consuming and expensive. In order to speed-up this work, a new parameter estimation approach for modelling ion-exchange chromatography in linear conditions was developed. It aims at reducing the time and protein demand for the model calibration. The method combines the estimation of kinetic and thermodynamic parameters based on the simultaneous variation of the gradient slope and the residence time in a set of five linear gradient elutions. The parameters are estimated from a Yamamoto plot and a gradient-adjusted Van Deemter plot. The combined approach increases the information extracted per experiment compared to the individual methods. As a proof of concept, the combined approach was successfully applied for a monoclonal antibody on a cation-exchanger and for a Fc-fusion protein on an anion-exchange resin. The individual parameter estimations for the mAb confirmed that the new approach maintained the accuracy of the usual Yamamoto and Van Deemter plots. In the second case, offline size-exclusion chromatography was performed in order to estimate the thermodynamic parameters of an impurity (high molecular weight species) simultaneously with the main product. Finally, the parameters obtained from the combined approach were used in a lumped kinetic model to simulate the chromatography runs. The simulated chromatograms obtained for a wide range of gradient lengths and residence times showed only small deviations compared to the experimental data. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular statics simulation of CdTe grain boundary structures and energetics using a bond-order potential

NASA Astrophysics Data System (ADS)

Stechmann, Guillaume; Zaefferer, Stefan; Raabe, Dierk

2018-06-01

The structure and energetics of coincidence site lattice grain boundaries (GB) in CdTe are investigated by mean of molecular statics simulations, using the Cd–Zn–Te bond-order potential (second iteration) developed by Ward et al (2012 Phys. Rev. B 86 245203; 2013 J. Mol. Modelling 19 5469–77). The effects of misorientation (Σ value) and interface plane are treated separately, complying with the critical need for full five-parameter characterization of GB. In addition, stoichiometric shifts, occurring between the inner interfaces and their adjacent atomic layers, are also predicted, revealing the energetic preference of Te-rich boundaries, opening opportunities for crystallography-based intrinsic interface doping. Our results also suggest that the intuitive assumption that Σ3 boundaries with low-indexed planes are more energetically favorable is often unfounded, except for coherent twins developing on {111} boundary planes. Therefore, Σ5, 7 or 9 boundaries, with lower interface energy than that of twin boundaries lying on different facets, are frequently encountered.

Evaluation of tocopherol recovery through simulation of molecular distillation process.

PubMed

Moraes, E B; Batistella, C B; Alvarez, M E Torres; Filho, Rubens Maciel; Maciel, M R Wolf

2004-01-01

DISMOL simulator was used to determine the best possible operating conditions to guide, in future studies, experimental works. This simulator needs several physical-chemical properties and often it is very difficult to determine them because of the complexity of the involved components. Their determinations must be made through correlations and/or predictions, in order to characterize the system and calculate it. The first try is to have simulation results of a system that later can be validated with experimental data. To implement, in the simulator, the necessary parameters of complex systems is a difficult task. In this work, we aimed to determe these properties in order to evaluate the tocopherol (vitamin E) recovery using a DISMOL simulator. The raw material used was the crude deodorizer distillate of soya oil. With this procedure, it is possible to determine the best operating conditions for experimental works and to evaluate the process in the separation of new systems, analyzing the profiles obtained from these simulations for the falling film molecular distillator.

Molecular dynamics simulations of a DMSO/water mixture using the AMBER force field.

PubMed

Stachura, Slawomir S; Malajczuk, Chris J; Mancera, Ricardo L

2018-06-25

Due to its protective properties of biological samples at low temperatures and under desiccation, dimethyl sulfoxide (DMSO) in aqueous solutions has been studied widely by many experimental approaches and molecular dynamics (MD) simulations. In the case of the latter, AMBER is among the most commonly used force fields for simulations of biomolecular systems; however, the parameters for DMSO published by Fox and Kollman in 1998 have only been tested for pure liquid DMSO. We have conducted an MD simulation study of DMSO in a water mixture and computed several structural and dynamical properties such as of the mean density, self-diffusion coefficient, hydrogen bonding and DMSO and water ordering. The AMBER force field of DMSO is seen to reproduce well most of the experimental properties of DMSO in water, with the mixture displaying strong and specific water ordering, as observed in experiments and multiple other MD simulations with other non-polarizable force fields. Graphical abstract Hydration structure within hydrogen-bonding distance around a DMSOmolecule.

The Effect of Molecular Orientation to Solid-Solid and Melting Transitions

NASA Astrophysics Data System (ADS)

Yazici, Mustafa; Özgan, Şükrü

The thermodynamics of solid-solid and solid-liquid transitions are investigated with an account of the number of molecular orientation. The variations of the positional and orientational orders with the reduced temperature are studied. It is found out that orientational order parameter is very sensitive to the number of allowed orientation. The reduced transition temperatures, volume changes and entropy changes of the phase transitions and theoretical phase diagrams are obtained. The entropy changes of melting transitions for different numbers of allowed orientation of the present model are compared with the theoretical results and some experimental data. The quantitative predictions of the model are compared with experimental results for plastic crystals and agreement between predictions of the model and the experimental results are approximately good. Also, different numbers of allowed orientation D correspond to different experimental results HI, HBr, H2S for D = 2; HBr, CCl4, HI for D = 4; C2H12 for D = 6; CH4, PH3 for D = 20.

Anomalous temperature dependence of layer spacing of de Vries liquid crystals: Compensation model

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

Merkel, K.; Kocot, A.; Vij, J. K., E-mail: jvij@tcd.ie

Smectic liquid crystals that exhibit temperature independent layer thickness offer technological advantages for their use in displays and photonic devices. The dependence of the layer spacing in SmA and SmC phases of de Vries liquid crystals is found to exhibit distinct features. On entering the SmC phase, the layer thickness initially decreases below SmA to SmC (T{sub A–C}) transition temperature but increases anomalously with reducing temperature despite the molecular tilt increasing. This anomalous observation is being explained quantitatively. Results of IR spectroscopy show that layer shrinkage is caused by tilt of the mesogen's rigid core, whereas the expansion is causedmore » by the chains getting more ordered with reducing temperature. This mutual compensation arising from molecular fragments contributing to the layer thickness differs from the previous models. The orientational order parameter of the rigid core of the mesogen provides direct evidence for de Vries cone model in the SmA phase for the two compounds investigated.« less

Predicting the nonlinear optical response in the resonant region from the linear characterization: a self-consistent theory for the first-, second-, and third-order (non)linear optical response

NASA Astrophysics Data System (ADS)

Pérez-Moreno, Javier; Clays, Koen; Kuzyk, Mark G.

2010-08-01

We introduce a self-consistent theory for the description of the optical linear and nonlinear response of molecules that is based strictly on the results of the experimental characterization. We show how the Thomas-Kuhn sum-rules can be used to eliminate the dependence of the nonlinear response on parameters that are not directly measurable. Our approach leads to the successful modeling of the dispersion of the nonlinear response of complex molecular structures with different geometries (dipolar and octupolar), and can be used as a guide towards the modeling in terms of fundamental physical parameters.

Temporal behavior of RHEED intensity oscillations during molecular beam epitaxial growth of GaAs and AlGaAs on (111)B GaAs substrates

NASA Astrophysics Data System (ADS)

Yen, Ming Y.; Haas, T. W.

1990-10-01

We present the temporal behavior of intensity oscillations in reflection high-energy electron diffraction (RHEED) during molecular beam epitaxial (MBE) growth of GaAs and A1GaAs on (1 1 1)B GaAs substrates. The RHEED intensity oscillations were examined as a function of growth parameters in order to provide the insight into the dynamic characteristics and to identify the optimal condition for the two-dimensional layer-by-layer growth. The most intense RHEED oscillation was found to occur within a very narrow temperature range which seems to optimize the surface migration kinetics of the arriving group III elements and the molecular dissodiative reaction of the group V elements. The appearance of an initial transient of the intensity upon commencement of the growth and its implications are described.

Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

NASA Technical Reports Server (NTRS)

Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

2001-01-01

Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

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

NONE

In order to develop the conditions for preparing polymers with different molecular masses, the authors continued their investigation of TMSP (1-(trimethylsilyl)-1-propyne) polymerization catalyzed by TaCl{sub 5} and TaCl{sub 5}/BuLi at various ratios of VTMS (regulator of molecular mass of the polymer) : catalyst. They also studied the effect of the structure of silahydrocarbon on the process of TMSP polymerization. To this end, they carried out polymerization of TMSP in the presence of additives of vinylphenyldimethylsilane and vinylallyldimethylsilane. The conditions of experiments and the results obtained are shown. The method for controlling the molecular mass of PTMSP makes it possible tomore » prepare PTMSP suitable for manufacture of both flat membranes and hollow fibers. The paper also describes the experimental study of PTMSP gas permeability, gas sorption in PTMSP, and a computer program for the prediction of all gas permeability parameters of polymers.« less

Atomic concentration effect on thermal properties during solidification of Pt-Rh alloy: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Yildiz, A. K.; Celik, F. A.

2017-04-01

The solidification process of Platinum-Rhodium alloy from liquid phase to solid state is investigated at the nano-scale by using Molecular Dynamics Simulation (MDS) for different atomic concentration ratios of Pt. The critical nucleus radius, the bond order parameter, interfacial free energies and total energy based on nucleation theory of the alloy are examined with respect to the temperature changes. The heat of fusion from high temperatures to low temperatures during solidification of the alloy system is determined from molecular dynamics simulation. The structural development is determined from the radial distribution function. It is observed from the results that the melting point of the alloy system decreases with increasing concentration of Pt and that variation of Pt ratio in the alloy shows a remarkable effect on solidification to understand the cooling process of thermal effects.

Sequential Injection Analysis for Optimization of Molecular Biology Reactions

PubMed Central

Allen, Peter B.; Ellington, Andrew D.

2011-01-01

In order to automate the optimization of complex biochemical and molecular biology reactions, we developed a Sequential Injection Analysis (SIA) device and combined this with a Design of Experiment (DOE) algorithm. This combination of hardware and software automatically explores the parameter space of the reaction and provides continuous feedback for optimizing reaction conditions. As an example, we optimized the endonuclease digest of a fluorogenic substrate, and showed that the optimized reaction conditions also applied to the digest of the substrate outside of the device, and to the digest of a plasmid. The sequential technique quickly arrived at optimized reaction conditions with less reagent use than a batch process (such as a fluid handling robot exploring multiple reaction conditions in parallel) would have. The device and method should now be amenable to much more complex molecular biology reactions whose variable spaces are correspondingly larger. PMID:21338059

Viscoelasticity imaging using ultrasound: parameters and error analysis

PubMed Central

Sridhar, M; Liu, J

2009-01-01

Techniques are being developed to image viscoelastic features of soft tissues from time-varying strain. A compress-hold-release stress stimulus commonly used in creep-recovery measurements is applied to samples to form images of elastic strain and strain retardance times. While the intended application is diagnostic breast imaging, results in gelatin hydrogels are presented to demonstrate the techniques. The spatiotemporal behaviour of gelatin is described by linear viscoelastic theory formulated for polymeric solids. Measured creep responses of polymers are frequently modelled as sums of exponentials whose time constants describe the delay or retardation of the full strain response. We found the spectrum of retardation times τ to be continuous and bimodal, where the amplitude at each τ represents the relative number of molecular bonds with a given strength and conformation. Such spectra indicate that the molecular weight of the polymer fibres between bonding points is large. Imaging parameters are found by summarizing these complex spectral distributions at each location in the medium with a second-order Voigt rheological model. This simplification reduces the dimensionality of the data for selecting imaging parameters while preserving essential information on how the creeping deformation describes fluid flow and collagen matrix restructuring in the medium. The focus of this paper is on imaging parameter estimation from ultrasonic echo data, and how jitter from hand-held force applicators used for clinical applications propagate through the imaging chain to generate image noise. PMID:17440244

Microwave dielectric relaxation spectroscopy study of propylene glycol/ethanol binary mixtures: Temperature dependence

NASA Astrophysics Data System (ADS)

Vishwam, T.; Shihab, Suriya; Murthy, V. R. K.; Tiong, Ha Sie; Sreehari Sastry, S.

2017-05-01

Complex dielectric permittivity measurements of propylene glycol (PG) in ethanol at various mole fractions were measured by using open-ended coaxial probe technique at different temperatures in the frequency range 0.02 < ν/GHz < 20. The dipole moment (μ), excess dipole moment (Δμ),excess permittivity (εE), excess inverse relaxation time(1/τ)E, Bruggeman parameter (fB), excess Helmholtz energy (ΔFE) are determined using experimental data. From the minimum energy based geometry optimization, dipole moments of individual monomers of propylene glycol and ethanol and their binary system have been evaluated theoretically at gaseous state as well as alcoholic medium by using PCM and IEFPCM solvation models from the Hatree-Fock (HF) and Density Functional Theory (DFT-B3LYP) methods with 6-311G* and 6-311G** basis sets. The obtained results have been interpreted in terms of the short and long range ordering of the dipoles, Kirkwood correlation factor (geff), thermodynamic parameters, mean molecular polarizability (αM) and interaction in the mixture through hydrogen bonding. Dielectric relaxation study of propylene glycol in ethanol medium Determination of excess dielectric and thermodynamic parameters Comparison of experimental dipole moment with theoretical calculations Interpretation of the molecular interactions in the liquid through H-bonding Correlation between the evaluated dielectric parameters and theoretical results

Reparameterization of All-Atom Dipalmitoylphosphatidylcholine Lipid Parameters Enables Simulation of Fluid Bilayers at Zero Tension

PubMed Central

Sonne, Jacob; Jensen, Morten Ø.; Hansen, Flemming Y.; Hemmingsen, Lars; Peters, Günther H.

2007-01-01

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ∼48 Å2. To obtain fluid (Lα) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field. PMID:17400696

Liquid crystalline phases in suspensions of pigments in non-polar solvents

NASA Astrophysics Data System (ADS)

Klein, Susanne; Richardson, Robert M.; Eremin, Alexey

We will discuss colloid suspensions of pigments and compare their electro-optic properties with those of traditional dyed low molecular weight liquid crystal systems. There are several potential advantages of colloidal suspensions over low molecular weight liquid crystal systems: a very high contrast because of the high orientational order parameter of suspensions of rod shaped nano-particles, the excellent light fastness of pigments as compared to dyes and high colour saturations resulting from the high loading of the colour stuff. Although a weak `single-particle' electro-optic response can be observed in dilute suspensions, the response is very much enhanced when the concentration of the particles is sufficient to lead to a nematic phase. Excellent stability of suspensions is beneficial for experimental observation and reproducibility, but it is a fundamental necessity for display applications. We therefore discuss a method to achieve long term stability of dispersed pigments and the reasons for its success. Small angle X-ray scattering was used to determine the orientational order parameter of the suspensions as a function of concentration and the dynamic response to an applied electric field. Optical properties were investigated for a wide range of pigment concentrations. Electro-optical phenomena, such as field-induced birefringence and switching, were characterised. In addition, mixtures of pigment suspensions with small amounts of ferrofluids show promise as future magneto-optical materials.

Indole Localization in an Explicit Bilayer Revealed via Molecular Dynamics

NASA Astrophysics Data System (ADS)

Norman, Kristen

2005-11-01

It is well known that the amino-acid tryptophan is particularly stable in the interfacial region of biological membranes, and this preference is a property of the tryptophan side-chain. Analogues of this side-chain, such as indole, strongly localize in the interfacial region, especially near the glycerol moiety of the lipids in the bilayer. Using molecular dynamics calculations, we determine the potential of mean force (PMF) for indoles in the bilayer. We compare the calculated PMF for indole with that of benzene to show that exclusion from the center of the lipid bilayer does not occur in all aromatics, but is strong in indoles. We find three minima in the PMF. Indole is most stabilized near the glycerol moiety. A weaker binding location is found near the choline groups of the lipid molecules. An even weaker binding side is found near the center of the lipid hydrocarbon core. Comparisions between uncharged, weakly charged, and highly charged indoles demonstrate that the exclusion is caused by the charge distribution on the indole rather than the ``lipo-phobic'' effect. High temperature simulations are used to determine the relative contribution of enthalpy and entropy to indole localization. The orientation of indole is found to be largely charge independent and is a strong function of depth within the bilayer. We find good agreement between simulated SCD order parameters for indole and experimentally determined order parameters.

Enhanced Electrical Conductivity of Molecularly p-Doped Poly(3-hexylthiophene) through Understanding the Correlation with Solid-State Order

PubMed Central

2017-01-01

Molecular p-doping of the conjugated polymer poly(3-hexylthiophene) (P3HT) with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) is a widely studied model system. Underlying structure–property relationships are poorly understood because processing and doping are often carried out simultaneously. Here, we exploit doping from the vapor phase, which allows us to disentangle the influence of processing and doping. Through this approach, we are able to establish how the electrical conductivity varies with regard to a series of predefined structural parameters. We demonstrate that improving the degree of solid-state order, which we control through the choice of processing solvent and regioregularity, strongly increases the electrical conductivity. As a result, we achieve a value of up to 12.7 S cm–1 for P3HT:F4TCNQ. We determine the F4TCNQ anion concentration and find that the number of (bound + mobile) charge carriers of about 10–4 mol cm–3 is not influenced by the degree of solid-state order. Thus, the observed increase in electrical conductivity by almost 2 orders of magnitude can be attributed to an increase in charge-carrier mobility to more than 10–1 cm2 V–1 s–1. Surprisingly, in contrast to charge transport in undoped P3HT, we find that the molecular weight of the polymer does not strongly influence the electrical conductivity, which highlights the need for studies that elucidate structure–property relationships of strongly doped conjugated polymers. PMID:29093606

Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches

PubMed Central

2011-01-01

Background Previously, the hypothetical protein, KPN00728 from Klebsiella pneumoniae MGH78578 was the Succinate dehydrogenase (SDH) chain C subunit via structural prediction and molecular docking simulation studies. However, due to limitation in docking simulation, an in-depth understanding of how SDH interaction occurs across the transmembrane of mitochondria could not be provided. Results In this present study, molecular dynamics (MD) simulation of KPN00728 and SDH chain D in a membrane was performed in order to gain a deeper insight into its molecular role as SDH. Structural stability was successfully obtained in the calculation for area per lipid, tail order parameter, thickness of lipid and secondary structural properties. Interestingly, water molecules were found to be highly possible in mediating the interaction between Ubiquinone (UQ) and SDH chain C via interaction with Ser27 and Arg31 residues as compared with earlier docking study. Polar residues such as Asp95 and Glu101 (KPN00728), Asp15 and Glu78 (SDH chain D) might have contributed in the creation of a polar environment which is essential for electron transport chain in Krebs cycle. Conclusions As a conclusion, a part from the structural stability comparability, the dynamic of the interacting residues and hydrogen bonding analysis had further proved that the interaction of KPN00728 as SDH is preserved and well agreed with our postulation earlier. PMID:22372825

Theory of Excitation Transfer between Two-Dimensional Semiconductor and Molecular Layers

NASA Astrophysics Data System (ADS)

Specht, Judith F.; Verdenhalven, Eike; Bieniek, Björn; Rinke, Patrick; Knorr, Andreas; Richter, Marten

2018-04-01

The geometry-dependent energy transfer rate from an electrically pumped inorganic semiconductor quantum well into an organic molecular layer is studied theoretically. We focus on Förster-type nonradiative excitation transfer between the organic and inorganic layers and include quasimomentum conservation and intermolecular coupling between the molecules in the organic film. (Transition) partial charges calculated from density-functional theory are used to calculate the coupling elements. The partial charges describe the spatial charge distribution and go beyond the common dipole-dipole interaction. We find that the transfer rates are highly sensitive to variations in the geometry of the hybrid inorganic-organic system. For instance, the transfer efficiency is improved by up to 2 orders of magnitude by tuning the spatial arrangement of the molecules on the surface: Parameters of importance are the molecular packing density along the effective molecular dipole axis and the distance between the molecules and the surface. We also observe that the device performance strongly depends on the orientation of the molecular dipole moments relative to the substrate dipole moments determined by the inorganic crystal structure. Moreover, the operating regime is identified where inscattering dominates over unwanted backscattering from the molecular layer into the substrate.

Orientation and Order of the Amide Group of Sphingomyelin in Bilayers Determined by Solid-State NMR

PubMed Central

Matsumori, Nobuaki; Yamaguchi, Toshiyuki; Maeta, Yoshiko; Murata, Michio

2015-01-01

Sphingomyelin (SM) and cholesterol (Chol) are considered essential for the formation of lipid rafts; however, the types of molecular interactions involved in this process, such as intermolecular hydrogen bonding, are not well understood. Since, unlike other phospholipids, SM is characterized by the presence of an amide group, it is essential to determine the orientation of the amide and its order in the lipid bilayers to understand the nature of the hydrogen bonds in lipid rafts. For this study, 1′-13C-2-15N-labeled and 2′-13C-2-15N-labeled SMs were prepared, and the rotational-axis direction and order parameters of the SM amide in bilayers were determined based on 13C and 15N chemical-shift anisotropies and intramolecular 13C-15N dipole coupling constants. Results revealed that the amide orientation was minimally affected by Chol, whereas the order was enhanced significantly in its presence. Thus, Chol likely promotes the formation of an intermolecular hydrogen-bond network involving the SM amide without significantly changing its orientation, providing a higher order to the SM amide. To our knowledge, this study offers new insight into the significance of the SM amide orientation with regard to molecular recognition in lipid rafts, and therefore provides a deeper understanding of the mechanism of their formation. PMID:26083921

Interpreting atom probe data from chromium oxide scales.

PubMed

La Fontaine, Alexandre; Gault, Baptiste; Breen, Andrew; Stephenson, Leigh; Ceguerra, Anna V; Yang, Limei; Nguyen, Thuan Dinh; Zhang, Jianqiang; Young, David J; Cairney, Julie M

2015-12-01

Picosecond-pulsed ultraviolet-laser (UV-355 nm) assisted atom probe tomography (APT) was used to analyze protective, thermally grown chromium oxides formed on stainless steel. The influence of analysis parameters on the thermal tail observed in the mass spectra and the chemical composition is investigated. A new parameter termed "laser sensitivity factor" is introduced in order to quantify the effect of laser energy on the extent of the thermal tail. This parameter is used to compare the effect of increasing laser energy on thermal tails in chromia and chromite samples. Also explored is the effect of increasing laser energy on the measured oxygen content and the effect of specimen base temperature and laser pulse frequency on the mass spectrum. Finally, we report a preliminary analysis of molecular ion dissociations in chromia. Copyright © 2015 Elsevier B.V. All rights reserved.

Interrogating selectivity in catalysis using molecular vibrations

NASA Astrophysics Data System (ADS)

Milo, Anat; Bess, Elizabeth N.; Sigman, Matthew S.

2014-03-01

The delineation of molecular properties that underlie reactivity and selectivity is at the core of physical organic chemistry, and this knowledge can be used to inform the design of improved synthetic methods or identify new chemical transformations. For this reason, the mathematical representation of properties affecting reactivity and selectivity trends, that is, molecular parameters, is paramount. Correlations produced by equating these molecular parameters with experimental outcomes are often defined as free-energy relationships and can be used to evaluate the origin of selectivity and to generate new, experimentally testable hypotheses. The premise behind successful correlations of this type is that a systematically perturbed molecular property affects a transition-state interaction between the catalyst, substrate and any reaction components involved in the determination of selectivity. Classic physical organic molecular descriptors, such as Hammett, Taft or Charton parameters, seek to independently probe isolated electronic or steric effects. However, these parameters cannot address simultaneous, non-additive variations to more than one molecular property, which limits their utility. Here we report a parameter system based on the vibrational response of a molecule to infrared radiation that can be used to mathematically model and predict selectivity trends for reactions with interlinked steric and electronic effects at positions of interest. The disclosed parameter system is mechanistically derived and should find broad use in the study of chemical and biological systems.

A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement-Förster-Type Resonance Energy Transfer (PIFE-FRET).

PubMed

Lerner, Eitan; Ploetz, Evelyn; Hohlbein, Johannes; Cordes, Thorben; Weiss, Shimon

2016-07-07

Single-molecule, protein-induced fluorescence enhancement (PIFE) serves as a molecular ruler at molecular distances inaccessible to other spectroscopic rulers such as Förster-type resonance energy transfer (FRET) or photoinduced electron transfer. In order to provide two simultaneous measurements of two distances on different molecular length scales for the analysis of macromolecular complexes, we and others recently combined measurements of PIFE and FRET (PIFE-FRET) on the single molecule level. PIFE relies on steric hindrance of the fluorophore Cy3, which is covalently attached to a biomolecule of interest, to rotate out of an excited-state trans isomer to the cis isomer through a 90° intermediate. In this work, we provide a theoretical framework that accounts for relevant photophysical and kinetic parameters of PIFE-FRET, show how this framework allows the extraction of the fold-decrease in isomerization mobility from experimental data, and show how these results provide information on changes in the accessible volume of Cy3. The utility of this model is then demonstrated for experimental results on PIFE-FRET measurement of different protein-DNA interactions. The proposed model and extracted parameters could serve as a benchmark to allow quantitative comparison of PIFE effects in different biological systems.

Influence of Illumination on the Electrical Properties of p-(ZnMgTe/ZnTe:N)/CdTe/n-(CdTe:I)/GaAs Heterojunction Grown by Molecular Beam Epitaxy (MBE)

NASA Astrophysics Data System (ADS)

Jum'h, I.; Abd El-Sadek, M. S.; Al-Taani, H.; Yahia, I. S.; Karczewski, G.

2017-02-01

Heterostructure p-(ZnMgTe/ZnTe:N)/CdTe/n-(CdTe:I)/GaAs was evaporated using molecular beam epitaxy and investigated for photovoltaic energy conversion application. The electrical properties of the studied heterostructure were measured and characterized in order to understand the relevant electrical transport mechanisms. Electrical properties derived from the current-voltage ( I- V) characteristics of solar cells provide essential information necessary for the analysis of performance losses and device efficiency. I- V characteristics are investigated in dark conditions and under different light intensities. All the electrical and power parameters of the heterostructure were measured, calculated and explained.

Molecular dynamics simulation of liquid structure for undercooled Zr-Nb alloys assisted with electrostatic levitation experiments

NASA Astrophysics Data System (ADS)

Yang, S. J.; Hu, L.; Wang, L.; Wei, B.

2018-06-01

The liquid structures of undercooled Zr90Nb10, Zr70Nb30 and Zr50Nb50 alloys were studied by molecular dynamics simulation combined with electrostatic levitation experiments. The densities of three alloys were measured by electrostatic levitation to modify the Zr-Nb potential functions by adjusting parameters in potential functions. In simulation, the atomic packing in Zr-Nb alloys was more ordered at lower temperatures. The Voronoi tessellation analyses indicated Nb-centered clusters were easier to form than Zr-centered clusters although the Nb content was less than 50%. The partial pair distribution functions showed that the interactions among Zr atoms are quite different to that among Nb atoms.

Evolution of bacterial virulence.

PubMed

Diard, Médéric; Hardt, Wolf-Dietrich

2017-09-01

Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population. We review both approaches and discuss how they can complement each other in order to obtain a comprehensive understanding of bacterial virulence, its emergence, maintenance and evolution. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A trough for improved SFG spectroscopy of lipid monolayers.

PubMed

Franz, Johannes; van Zadel, Marc-Jan; Weidner, Tobias

2017-05-01

Lipid monolayers are indispensable model systems for biological membranes. The main advantage over bilayer model systems is that the surface pressure within the layer can be directly and reliably controlled. The sensitive interplay between surface pressure and temperature determines the molecular order within a model membrane and consequently determines the membrane phase behavior. The lipid phase is of crucial importance for a range of membrane functions such as protein interactions and membrane permeability. A very reliable method to probe the structure of lipid monolayers is sum frequency generation (SFG) vibrational spectroscopy. Not only is SFG extremely surface sensitive but it can also directly access critical parameters such as lipid order and orientation, and it can provide valuable information about protein interactions along with interfacial hydration. However, recent studies have shown that temperature gradients caused by high power laser beams perturb the lipid layers and potentially obscure the spectroscopic results. Here we demonstrate how the local heating problem can be effectively reduced by spatially distributing the laser pulses on the sample surface using a translating Langmuir trough for SFG experiments at lipid monolayers. The efficiency of the trough is illustrated by the detection of enhanced molecular order due to reduced heat load.

A trough for improved SFG spectroscopy of lipid monolayers

NASA Astrophysics Data System (ADS)

Franz, Johannes; van Zadel, Marc-Jan; Weidner, Tobias

2017-05-01

Lipid monolayers are indispensable model systems for biological membranes. The main advantage over bilayer model systems is that the surface pressure within the layer can be directly and reliably controlled. The sensitive interplay between surface pressure and temperature determines the molecular order within a model membrane and consequently determines the membrane phase behavior. The lipid phase is of crucial importance for a range of membrane functions such as protein interactions and membrane permeability. A very reliable method to probe the structure of lipid monolayers is sum frequency generation (SFG) vibrational spectroscopy. Not only is SFG extremely surface sensitive but it can also directly access critical parameters such as lipid order and orientation, and it can provide valuable information about protein interactions along with interfacial hydration. However, recent studies have shown that temperature gradients caused by high power laser beams perturb the lipid layers and potentially obscure the spectroscopic results. Here we demonstrate how the local heating problem can be effectively reduced by spatially distributing the laser pulses on the sample surface using a translating Langmuir trough for SFG experiments at lipid monolayers. The efficiency of the trough is illustrated by the detection of enhanced molecular order due to reduced heat load.

Phototropic liquid crystal materials containing naphthopyran dopants

NASA Astrophysics Data System (ADS)

Rumi, Mariacristina; Cazzell, Seth; Kosa, Tamas; Sukhomlinova, Ludmila; Taheri, Bahman; Bunning, Timothy; White, Timothy

2015-03-01

Dopant molecules dispersed in a liquid crystalline material usually affects the order of the system and the transition temperature between various phases. If the dopants undergo photoisomerization between conformers with different shapes, the interactions with the liquid crystal molecules can be different for the material in the dark and during exposure to light of appropriate wavelength. This can be used to achieve isothermal photoinduced phase transitions (phototropism). With proper selection of materials components, both order-to-disorder and disorder-to-order photoinduced transition have been demonstrated. Isothermal order-increasing transitions have been observed recently using naphthopyran derivatives as dopants. We are investigating the changes in order parameter and transition temperature of liquid crystal mixtures containing naphthopyrans and how they are related to exposure conditions and to the concentration and molecular structure of the dopants. We are also studying the nature of the photoinduced phase transitions, and comparing the behavior with that of azobenzene-doped mixtures, in which exposure to light leads to a decrease, instead of an increase, in the order of the system.

Prediction of quantum interference in molecular junctions using a parabolic diagram: Understanding the origin of Fano and anti- resonances

NASA Astrophysics Data System (ADS)

Nozaki, Daijiro; Avdoshenko, Stanislav M.; Sevinçli, Hâldun; Gutierrez, Rafael; Cuniberti, Gianaurelio

2013-03-01

Recently the interest in quantum interference (QI) phenomena in molecular devices (molecular junctions) has been growing due to the unique features observed in the transmission spectra. In order to design single molecular devices exploiting QI effects as desired, it is necessary to provide simple rules for predicting the appearance of QI effects such as anti-resonances or Fano line shapes and for controlling them. In this study, we derive a transmission function of a generic molecular junction with a side group (T-shaped molecular junction) using a minimal toy model. We developed a simple method to predict the appearance of quantum interference, Fano resonances or anti- resonances, and its position in the conductance spectrum by introducing a simple graphical representation (parabolic model). Using it we can easily visualize the relation between the key electronic parameters and the positions of normal resonant peaks and anti-resonant peaks induced by quantum interference in the conductance spectrum. We also demonstrate Fano and anti-resonance in T-shaped molecular junctions using a simple tight-binding model. This parabolic model enables one to infer on-site energies of T-shaped molecules and the coupling between side group and main conduction channel from transmission spectra.

Solid-solid collapse transition in a two dimensional model molecular system.

PubMed

Singh, Rakesh S; Bagchi, Biman

2013-11-21

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Solid-solid collapse transition in a two dimensional model molecular system

NASA Astrophysics Data System (ADS)

Singh, Rakesh S.; Bagchi, Biman

2013-11-01

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains.

Glass transition of polymers in bulk, confined geometries, and near interfaces

NASA Astrophysics Data System (ADS)

Napolitano, Simone; Glynos, Emmanouil; Tito, Nicholas B.

2017-03-01

When cooled or pressurized, polymer melts exhibit a tremendous reduction in molecular mobility. If the process is performed at a constant rate, the structural relaxation time of the liquid eventually exceeds the time allowed for equilibration. This brings the system out of equilibrium, and the liquid is operationally defined as a glass—a solid lacking long-range order. Despite almost 100 years of research on the (liquid/)glass transition, it is not yet clear which molecular mechanisms are responsible for the unique slow-down in molecular dynamics. In this review, we first introduce the reader to experimental methodologies, theories, and simulations of glassy polymer dynamics and vitrification. We then analyse the impact of connectivity, structure, and chain environment on molecular motion at the length scale of a few monomers, as well as how macromolecular architecture affects the glass transition of non-linear polymers. We then discuss a revised picture of nanoconfinement, going beyond a simple picture based on interfacial interactions and surface/volume ratio. Analysis of a large body of experimental evidence, results from molecular simulations, and predictions from theory supports, instead, a more complex framework where other parameters are relevant. We focus discussion specifically on local order, free volume, irreversible chain adsorption, the Debye-Waller factor of confined and confining media, chain rigidity, and the absolute value of the vitrification temperature. We end by highlighting the molecular origin of distributions in relaxation times and glass transition temperatures which exceed, by far, the size of a chain. Fast relaxation modes, almost universally present at the free surface between polymer and air, are also remarked upon. These modes relax at rates far larger than those characteristic of glassy dynamics in bulk. We speculate on how these may be a signature of unique relaxation processes occurring in confined or heterogeneous polymeric systems.

Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses.

PubMed

Smith, Kyle C; Weaver, James C

2011-08-19

Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. Copyright © 2011 Elsevier Inc. All rights reserved.

Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses

PubMed Central

Smith, Kyle C.; Weaver, James C.

2012-01-01

Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (~16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. PMID:21756883

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Non-equilibrium phase transitions in a liquid crystal

NASA Astrophysics Data System (ADS)

Dan, K.; Roy, M.; Datta, A.

2015-09-01

The present manuscript describes kinetic behaviour of the glass transition and non-equilibrium features of the "Nematic-Isotropic" (N-I) phase transition of a well known liquid crystalline material N-(4-methoxybenzylidene)-4-butylaniline from the effects of heating rate and initial temperature on the transitions, through differential scanning calorimetry (DSC), Fourier transform infrared and fluorescence spectroscopy. Around the vicinity of the glass transition temperature (Tg), while only a change in the baseline of the ΔCp vs T curve is observed for heating rate (β) > 5 K min-1, consistent with a glass transition, a clear peak for β ≤ 5 K min-1 and the rapid reduction in the ΔCp value from the former to the latter rate correspond to an order-disorder transition and a transition from ergodic to non-ergodic behaviour. The ln β vs 1000/T curve for the glass transition shows convex Arrhenius behaviour that can be explained very well by a purely entropic activation barrier [Dan et al., Eur. Phys. Lett. 108, 36007 (2014)]. Fourier transform infrared spectroscopy indicates sudden freezing of the out-of-plane distortion vibrations of the benzene rings around the glass transition temperature and a considerable red shift indicating enhanced coplanarity of the benzene rings and, consequently, enhancement in the molecular ordering compared to room temperature. We further provide a direct experimental evidence of the non-equilibrium nature of the N-I transition through the dependence of this transition temperature (TNI) and associated enthalpy change (ΔH) on the initial temperature (at fixed β-values) for the DSC scans. A plausible qualitative explanation based on Mesquita's extension of Landau-deGennes theory [O. N. de Mesquita, Braz. J. Phys. 28, 257 (1998)] has been put forward. The change in the molecular ordering from nematic to isotropic phase has been investigated through fluorescence anisotropy measurements where the order parameter, quantified by the anisotropy, goes to zero from nematic to isotropic phase. To a point below the transition temperature, the order parameter is constant but decreases linearly with increase in temperature below that indicating the dependence of nematic ordering on the initial temperature during heating consistent with the non-equilibrium nature of nematic-isotropic phase transition.

Dependence of short and intermediate-range order on preparation in experimental and modeled pure a-Si

DOE PAGES

Holmstrom, Eero; Haberl, Bianca; Pakarinen, Olli H.; ...

2016-02-20

Variability in the short-to-intermediate range order of pure amorphous silicon prepared by different experimental and computational techniques is probed by measuring mass density, atomic coordination, bond-angle deviation, and dihedral angle deviation. It is found that there is significant variability in order parameters at these length scales in this archetypal covalently bonded, monoatomic system. This diversity strongly reflects preparation technique and thermal history in both experimental and simulated systems. Experiment and simulation do not fully quantitatively agree, partly due to differences in the way parameters are accessed. However, qualitative agreement in the trends is identified. Relaxed forms of amorphous silicon closelymore » resemble continuous random networks generated by a hybrid method of bond-switching Monte Carlo and molecular dynamics simulation. As-prepared ion implanted amorphous silicon can be adequately modeled using a structure generated from amorphization via ion bombardement using energetic recoils. Preparation methods which narrowly avoid crystallization such as experimental pressure-induced amorphization or simulated melt-quenching result in inhomogeneous structures that contain regions with significant variations in atomic ordering. Ad hoc simulated structures containing small (1 nm) diamond cubic crystal inclusions were found to possess relatively high bond-angle deviations and low dihedral angle deviations, a trend that could not be reconciled with any experimental material.« less

X-ray and Raman scattering study of orientational order in nematic and heliconical nematic liquid crystals.

PubMed

Singh, Gautam; Fu, Jinxin; Agra-Kooijman, Dena M; Song, Jang-Kun; Vengatesan, M R; Srinivasarao, Mohan; Fisch, Michael R; Kumar, Satyendra

2016-12-01

The temperature dependence of the orientational order parameters 〈P_{2}(cosβ)〉 and 〈P_{4}(cosβ)〉 in the nematic (N) and twist-bend nematic (N_{tb}) phases of the liquid crystal dimer CB7CB have been measured using x-ray and polarized Raman scattering. The 〈P_{2}(cosβ)〉 obtained from both techniques are the same, while 〈P_{4}(cosβ)〉, determined by Raman scattering is, as expected, systematically larger than its x-ray value. Both order parameters increase in the N phase with decreasing temperature, drop across the N-N_{tb} transition, and continue to decrease. In the N_{tb} phase, the x-ray value of 〈P_{4}(cosβ)〉 eventually becomes negative, providing a direct and independent confirmation of a conical molecular orientational distribution. The heliconical tilt angle α, determined from orientational distribution functions in the N_{tb} phase, increases to ∼24^{∘} at ∼15 K below the transition. In the N_{tb} phase, α(T)∝(T^{*}-T)^{λ}, with λ=0.19±0.03. The transition supercools by 1.7 K, consistent with its weakly first-order nature. The value of λ is close to 0.25 indicating close proximity to a tricritical point.

Molecular structural property and potential energy dependence on nonequilibrium-thermodynamic state point of liquid n-hexadecane under shear.

PubMed

Tseng, Huan-Chang; Chang, Rong-Yeu; Wu, Jiann-Shing

2011-01-28

Extensive computer experiments have been conducted in order to shed light on the macroscopic shear flow behavior of liquid n-hexadecane fluid under isobaric-isothermal conditions through the nonequilibrium molecular dynamic methodology. With respect to shear rates, the accompanying variations in structural properties of the fluid span the microscopic range of understanding from the intrinsic to extrinsic characteristics. As drawn from the average value of bond length and bond angle, the distribution of dihedral angle, and the radius distribution function of intramolecular and intermolecular van der Waals distances, these intrinsic structures change with hardness, except in the situation of extreme shear rates. The shear-induced variation of thermodynamic state curve along with the shear rate studied is shown to consist of both the quasiequilibrium state plateau and the nonequilibrium-thermodynamic state slope. Significantly, the occurrence of nonequilibrium-thermodynamic state behavior is attributed to variations in molecular potential energies, which include bond stretching, bond bending, bond torsion, and intra- and intermolecular van der Waals interactions. To unfold the physical representation of extrinsic structural deformation, under the aggressive influence of a shear flow field, the molecular dimension and appearance can be directly described via the squared radius of gyration and the sphericity angle, R(g)(2) and ϕ, respectively. In addition, a specific orientational order S(x) defines the alignment of the molecules with the flow direction of the x-axis. As a result, at low shear rates, the overall molecules are slightly stretched and shaped in a manner that is increasingly ellipsoidal. Simultaneously, there is an obvious enhancement in the order. In contrast to high shear rates, the molecules spontaneously shrink themselves with a decreased value of R(g)(2), while their shape and order barely vary with an infinite value of ϕ and S(x). It is important to note that under different temperatures and pressures, these three parameters are integrated within a molecular description in response to thermodynamic state variable of density and rheological material function of shear viscosity.

Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems

PubMed Central

Schubert, Walter

2013-01-01

Understanding biological systems at the level of their relational (emergent) molecular properties in functional protein networks relies on imaging methods, able to spatially resolve a tissue or a cell as a giant, non-random, topologically defined collection of interacting supermolecules executing myriads of subcellular mechanisms. Here, the development and findings of parameter-unlimited functional super-resolution microscopy are described—a technology based on the fluorescence imaging cycler (IC) principle capable of co-mapping thousands of distinct biomolecular assemblies at high spatial resolution and differentiation (<40 nm distances). It is shown that the subcellular and transcellular features of such supermolecules can be described at the compositional and constitutional levels; that the spatial connection, relational stoichiometry, and topology of supermolecules generate hitherto unrecognized functional self-segmentation of biological tissues; that hierarchical features, common to thousands of simultaneously imaged supermolecules, can be identified; and how the resulting supramolecular order relates to spatial coding of cellular functionalities in biological systems. A large body of observations with IC molecular systems microscopy collected over 20 years have disclosed principles governed by a law of supramolecular segregation of cellular functionalities. This pervades phenomena, such as exceptional orderliness, functional selectivity, combinatorial and spatial periodicity, and hierarchical organization of large molecular systems, across all species investigated so far. This insight is based on the high degree of specificity, selectivity, and sensitivity of molecular recognition processes for fluorescence imaging beyond the spectral resolution limit, using probe libraries controlled by ICs. © 2013 The Authors. Journal of Molecular Recognition published by John Wiley & Sons, Ltd. PMID:24375580

Elasticity Imaging of Polymeric Media

PubMed Central

Sridhar, Mallika; Liu, Jie; Insana, Michael F.

2009-01-01

Viscoelastic properties of soft tissues and hydropolymers depend on the strength of molecular bonding forces connecting the polymer matrix and surrounding fluids. The basis for diagnostic imaging is that disease processes alter molecular-scale bonding in ways that vary the measurable stiffness and viscosity of the tissues. This paper reviews linear viscoelastic theory as applied to gelatin hydrogels for the purpose of formulating approaches to molecular-scale interpretation of elasticity imaging in soft biological tissues. Comparing measurements acquired under different geometries, we investigate the limitations of viscoelastic parameters acquired under various imaging conditions. Quasistatic (step-and-hold and low-frequency harmonic) stimuli applied to gels during creep and stress relaxation experiments in confined and unconfined geometries reveal continuous, bimodal distributions of respondance times. Within the linear range of responses, gelatin will behave more like a solid or fluid depending on the stimulus magnitude. Gelatin can be described statistically from a few parameters of low-order rheological models that form the basis of viscoelastic imaging. Unbiased estimates of imaging parameters are obtained only if creep data are acquired for greater than twice the highest retardance time constant and any steady-state viscous response has been eliminated. Elastic strain and retardance time images are found to provide the best combination of contrast and signal strength in gelatin. Retardance times indicate average behavior of fast (1–10 s) fluid flows and slow (50–400 s) matrix restructuring in response to the mechanical stimulus. Insofar as gelatin mimics other polymers, such as soft biological tissues, elasticity imaging can provide unique insights into complex structural and biochemical features of connectives tissues affected by disease. PMID:17408331

Molecular Imprinted Polymer of Methacrylic Acid Functionalised β-Cyclodextrin for Selective Removal of 2,4-Dichlorophenol

PubMed Central

Surikumaran, Hemavathy; Mohamad, Sharifah; Sarih, Norazilawati Muhamad

2014-01-01

This work describes methacrylic acid functionalized β-cyclodextrin (MAA-βCD) as a novel functional monomer in the preparation of molecular imprinted polymer (MIP MAA-βCD) for the selective removal of 2,4-dichlorophenol (2,4-DCP). The polymer was characterized using Fourier Transform Infrared (FTIR) spectroscopy, Brunauer-Emmett-Teller (BET) and Field Emission Scanning Electron Microscopy (FESEM) techniques. The influence of parameters such as solution pH, contact time, temperature and initial concentrations towards removal of 2,4-DCP using MIP MAA-βCD have been evaluated. The imprinted material shows fast kinetics and the optimum pH for removal of 2,4-DCP is pH 7. Compared with the corresponding non-imprinted polymer (NIP MAA-βCD), the MIP MAA-βCD exhibited higher adsorption capacity and outstanding selectivity towards 2,4-DCP. Freundlich isotherm best fitted the adsorption equilibrium data of MIP MAA-βCD and the kinetics followed a pseudo-second-order model. The calculated thermodynamic parameters showed that adsorption of 2,4-DCP was spontaneous and exothermic under the examined conditions. PMID:24727378

Localization of a microtubule organizing center by kinesin motors

NASA Astrophysics Data System (ADS)

Arita, Chikashi; Bosche, Jonas; Lück, Alexander; Santen, Ludger

2017-12-01

Molecular motors are proteins which bind to a polarized cytoskeletal filament and move steadily along it. Molecular motors of the kinesin family move along microtubules (MTs), which are a component of the cytoskeleton. A very processive kinesin motor Kip3p, is known to promote catastrophes and pausing of MT, in particular on cortical contact. These properties play an important role in positioning the mitotic spindle in budding yeast. We present a theoretical approach to positioning of MT networks under confinement. In order to explore a localization mechanism of a microtubule organizing center (MTOC), we introduce an idealized system of two MTs connected by a MTOC. The dynamics of Kip3p is modeled by interacting stochastic particles, which allows us to study the effects of motor-induced depolymerization in a finite volume. We find that localization in the middle of the cavity is realized in a parameter regime where the motor densities on the MTs are increasing with the distance from the MTOC. Localization at an asymmetric position is also possible by tuning model parameters.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

NASA Astrophysics Data System (ADS)

Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

PubMed

Cox, Courtney E; Phifer, Jeremy R; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T; O'Loughlin, Elizabeth J; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T; Paluch, Andrew S

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Atomistic Models of General Anesthetics for Use in in Silico Biological Studies

PubMed Central

2015-01-01

While small molecules have been used to induce anesthesia in a clinical setting for well over a century, a detailed understanding of the molecular mechanism remains elusive. In this study, we utilize ab initio calculations to develop a novel set of CHARMM-compatible parameters for the ubiquitous modern anesthetics desflurane, isoflurane, sevoflurane, and propofol for use in molecular dynamics (MD) simulations. The parameters generated were rigorously tested against known experimental physicochemical properties including dipole moment, density, enthalpy of vaporization, and free energy of solvation. In all cases, the anesthetic parameters were able to reproduce experimental measurements, signifying the robustness and accuracy of the atomistic models developed. The models were then used to study the interaction of anesthetics with the membrane. Calculation of the potential of mean force for inserting the molecules into a POPC bilayer revealed a distinct energetic minimum of 4–5 kcal/mol relative to aqueous solution at the level of the glycerol backbone in the membrane. The location of this minimum within the membrane suggests that anesthetics partition to the membrane prior to binding their ion channel targets, giving context to the Meyer–Overton correlation. Moreover, MD simulations of these drugs in the membrane give rise to computed membrane structural parameters, including atomic distribution, deuterium order parameters, dipole potential, and lateral stress profile, that indicate partitioning of anesthetics into the membrane at the concentration range studied here, which does not appear to perturb the structural integrity of the lipid bilayer. These results signify that an indirect, membrane-mediated mechanism of channel modulation is unlikely. PMID:25303275

A surface acoustic wave sensor functionalized with a polypyrrole molecularly imprinted polymer for selective dopamine detection.

PubMed

Maouche, Naima; Ktari, Nadia; Bakas, Idriss; Fourati, Najla; Zerrouki, Chouki; Seydou, Mahamadou; Maurel, François; Chehimi, Mohammed Mehdi

2015-11-01

A surface acoustic wave sensor operating at 104 MHz and functionalized with a polypyrrole molecularly imprinted polymer has been designed for selective detection of dopamine (DA). Optimization of pyrrole/DA ratio, polymerization and immersion times permitted to obtain a highly selective sensor, which has a sensitivity of 0.55°/mM (≈ 550 Hz/mM) and a detection limit of ≈ 10 nM. Morphology and related roughness parameters of molecularly imprinted polymer surfaces, before and after extraction of DA, as well as that of the non imprinted polymer were characterized by atomic force microscopy. The developed chemosensor selectively recognized dopamine over the structurally similar compound 4-hydroxyphenethylamine (referred as tyramine), or ascorbic acid,which co-exists with DA in body fluids at a much higher concentration. Selectivity tests were also carried out with dihydroxybenzene, for which an unexpected phase variation of order of 75% of the DA one was observed. Quantum chemical calculations, based on the density functional theory, were carried out to determine the nature of interactions between each analyte and the PPy matrix and the DA imprinted PPy polypyrrole sensing layer in order to account for the important phase variation observed during dihydroxybenzene injection. Copyright © 2015 John Wiley & Sons, Ltd.

Effects and mechanism of ultrasound pretreatment on rapeseed protein enzymolysis.

PubMed

Jin, Jian; Ma, Haile; Wang, Weiwei; Luo, Min; Wang, Bei; Qu, Wenjuan; He, Ronghai; Owusu, John; Li, Yunliang

2016-03-15

The disadvantages which stem from the use of traditional enzymolysis of protein has necessitated the need to employ sweeping frequency and pulsed ultrasound (SFPU) in the pretreatment of rapeseed protein prior to proteolysis in order to bring about improvement in enzymolysis efficiency. Further, in order to determine the mechanism of ultrasound-accelerated enzymolysis of RP, the effects of SFPU on the kinetics, thermodynamics, molecular conformation and microstructure of RP were investigated. Kinetic studies showed that SFPU pretreatment on RP improved enzymolysis by decreasing the apparent constant KM significantly (P < 0.05) by 32.8% and reducing the thermodynamic parameters Ea , ΔH and ΔS by 16.6%, 17.7% and 9.2% respectively. Fluorescence spectra revealed that SFPU pretreatment induced molecular unfolding, causing more hydrophobic groups and regions inside the molecules to be exposed to the outside. Circular dichroism analysis indicated that SFPU pretreatment decreased the α-helix content by 16.1% and increased the random coil content by 3.6%. In addition, scanning electron microscopy showed that SFPU pretreatment increased the specific surface area of RP. Ultrasound pretreatment is an efficient method in RP proteolysis to produce peptides through its impact on the molecular conformation and microstructure of proteins. © 2015 Society of Chemical Industry.

Relationship between thermodynamic parameter and thermodynamic scaling parameter for orientational relaxation time for flip-flop motion of nematic liquid crystals.

PubMed

Satoh, Katsuhiko

2013-03-07

Thermodynamic parameter Γ and thermodynamic scaling parameter γ for low-frequency relaxation time, which characterize flip-flop motion in a nematic phase, were verified by molecular dynamics simulation with a simple potential based on the Maier-Saupe theory. The parameter Γ, which is the slope of the logarithm for temperature and volume, was evaluated under various conditions at a wide range of temperatures, pressures, and volumes. To simulate thermodynamic scaling so that experimental data at isobaric, isothermal, and isochoric conditions can be rescaled onto a master curve with the parameters for some liquid crystal (LC) compounds, the relaxation time was evaluated from the first-rank orientational correlation function in the simulations, and thermodynamic scaling was verified with the simple potential representing small clusters. A possibility of an equivalence relationship between Γ and γ determined from the relaxation time in the simulation was assessed with available data from the experiments and simulations. In addition, an argument was proposed for the discrepancy between Γ and γ for some LCs in experiments: the discrepancy arises from disagreement of the value of the order parameter P2 rather than the constancy of relaxation time τ1(*) on pressure.

Magnon modes and magnon-vortex scattering in two-dimensional easy-plane ferromagnets

NASA Astrophysics Data System (ADS)

Ivanov, B. A.; Schnitzer, H. J.; Mertens, F. G.; Wysin, G. M.

1998-10-01

We calculate the magnon modes in the presence of a vortex on a circular system, combining analytical calculations in the continuum limit with a numerical diagonalization of the discrete system. The magnon modes are expressed by the S matrix for magnon-vortex scattering, as a function of the parameters and the size of the system and for different boundary conditions. Certain quasilocal translational modes are identified with the frequencies which appear in the trajectory X-->(t) of the vortex center in recent molecular dynamics simulations of the full many-spin model. Using these quasilocal modes we calculate the two parameters of a third-order equation of motion for X-->(t). This equation was recently derived by a collective variable theory and describes very well the trajectories observed in the simulations. Both parameters, the vortex mass and the factor in front of X-->⃛, depend strongly on the boundary conditions.

Low gravity synthesis of polymers with controlled molecular configuration

NASA Technical Reports Server (NTRS)

Heimbuch, A. H.; Parker, J. A.; Schindler, A.; Olf, H. G.

1975-01-01

Heterogeneous chemical systems have been studied for the synthesis of isotactic polypropylene in order to establish baseline parameters for the reaction process and to develop sensitive and accurate methods of analysis. These parameters and analytical methods may be used to make a comparison between the polypropylene obtained at one g with that of zero g (gravity). Baseline reaction parameters have been established for the slurry (liquid monomer in heptane/solid catalyst) polymerization of propylene to yield high purity, 98% isotactic polypropylene. Kinetic data for the slurry reaction showed that a sufficient quantity of polymer for complete characterization can be produced in a reaction time of 5 min; this time is compatible with that available on a sounding rocket for a zero-g simulation experiment. The preformed (activated) catalyst was found to be more reproducible in its activity than the in situ formed catalyst.

Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

NASA Astrophysics Data System (ADS)

Song, Yong-Shun; Shu, Yao-Gen; Zhou, Xin; Ou-Yang, Zhong-Can; Li, Ming

2017-01-01

The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models. However, all these models did not systematically investigate the dominant factor on DNAP fidelity, i.e. the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.

Finding a Potential Dipeptidyl Peptidase-4 (DPP-4) Inhibitor for Type-2 Diabetes Treatment Based on Molecular Docking, Pharmacophore Generation, and Molecular Dynamics Simulation

PubMed Central

Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J. P.; Chen, Yu-Ching

2016-01-01

Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes. PMID:27304951

Finding a Potential Dipeptidyl Peptidase-4 (DPP-4) Inhibitor for Type-2 Diabetes Treatment Based on Molecular Docking, Pharmacophore Generation, and Molecular Dynamics Simulation.

PubMed

Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J P; Chen, Yu-Ching

2016-06-13

Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes.

Distribution of Chains in Polymer Brushes Produced by a “Grafting From” Mechanism

DOE PAGES

Martinez, Andre P.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.; ...

2016-01-11

The molecular weight and polydispersity of the chains in a polymer brush are critical parameters determining the brush properties. However, the characterization of polymer brushes is hindered by the vanishingly small mass of polymer present in brush layers. In this study, in order to obtain sufficient quantities of polymer for analysis, polymer brushes were grown from high surface area fibrous nylon membranes by ATRP. We synthesized the brushes with varying surface initiator densities, polymerization times, and amounts of sacrificial initiator, then cleaved from the substrate, and analyzed by GPC and NMR. Characterization showed that the surface-grown polymer chains were moremore » polydisperse and had lower average molecular weight compared to solution-grown polymers synthesized concurrently. Furthermore, the molecular weight distribution of the polymer brushes was observed to be bimodal, with a low molecular weight population of chains representing a significant mass fraction of the polymer chains at high surface initiator densities. Moreover, the origin of this low MW polymer fraction is proposed to be the termination of growing chains by recombination during the early stages of polymerization, a mechanism confirmed by molecular dynamics simulations of brush polymerization.« less

Molecular dynamics simulations of single siloxane dendrimers: Molecular structure and intramolecular mobility of terminal groups

NASA Astrophysics Data System (ADS)

Kurbatov, A. O.; Balabaev, N. K.; Mazo, M. A.; Kramarenko, E. Yu.

2018-01-01

Molecular dynamics simulations of two types of isolated siloxane dendrimers of various generations (from the 2nd to the 8th) have been performed for temperatures ranging from 150 K to 600 K. The first type of dendrimer molecules has short spacers consisting of a single oxygen atom. In the dendrimers of the second type, spacers are longer and comprised of two oxygen atoms separated by a single silicon atom. A comparative analysis of molecular macroscopic parameters such as the gyration radius and the shape factor as well as atom distributions within dendrimer interior has been performed for varying generation number, temperature, and spacer length. It has been found that the short-spacer dendrimers of the 7th and 8th generations have a stressed central part with elongated bonds and deformed valence angles. Investigation of the time evolution of radial displacements of the terminal Si atoms has shown that a fraction of the Si groups have a reduced mobility. Therefore, rather long time trajectories (of the order of tens of nanoseconds) are required to study dendrimer intramolecular dynamics.

Current's Fluctuations through Molecular Wires Composed of Thiophene Rings.

PubMed

Ojeda Silva, Judith Helena; Cortés Peñaranda, Juan Camilo; Gómez Castaño, Jovanny A; Duque, Carlos Alberto

2018-04-11

We study theoretically the electronic transport and quantum fluctuations in single-molecule systems using thiophene rings as integrated elementary functions, as well as the dependence of these properties with the increase of the coupled rings, i.e., as a quantum wire. In order to analyze the current flow through these molecular systems, the thiophene rings are considered to be connected to metal contacts, which, in general terms, will be related to the application of voltages (bias voltages or gate voltages) to generate non-equilibrium behavior between the contacts. Due to the nonlinear behavior that is generated when said voltages are applied, it is possible to observe quantum fluctuations in the transport properties of these molecular wires. For the calculation of the transport properties, we applied a tight-binding approach using the Landauer-Büttiker formalism and the Fischer-Lee relationship, by means of a semi-analytic Green's function method within a real-space renormalization (decimation procedure). Our results showed an excellent agreement with results using a tight-binding model with a minimal number of parameters reported so far for these molecular systems.

Nano-particle drag prediction at low Reynolds number using a direct Boltzmann-BGK solution approach

NASA Astrophysics Data System (ADS)

Evans, B.

2018-01-01

This paper outlines a novel approach for solution of the Boltzmann-BGK equation describing molecular gas dynamics applied to the challenging problem of drag prediction of a 2D circular nano-particle at transitional Knudsen number (0.0214) and low Reynolds number (0.25-2.0). The numerical scheme utilises a discontinuous-Galerkin finite element discretisation for the physical space representing the problem particle geometry and a high order discretisation for molecular velocity space describing the molecular distribution function. The paper shows that this method produces drag predictions that are aligned well with the range of drag predictions for this problem generated from the alternative numerical approaches of molecular dynamics codes and a modified continuum scheme. It also demonstrates the sensitivity of flow-field solutions and therefore drag predictions to the wall absorption parameter used to construct the solid wall boundary condition used in the solver algorithm. The results from this work has applications in fields ranging from diagnostics and therapeutics in medicine to the fields of semiconductors and xerographics.

Systematic Analysis of Polymer Molecular Weight Influence on the Organic Photovoltaic Performance.

PubMed

Katsouras, Athanasios; Gasparini, Nicola; Koulogiannis, Chrysanthos; Spanos, Michael; Ameri, Tayebeh; Brabec, Christoph J; Chochos, Christos L; Avgeropoulos, Apostolos

2015-10-01

The molecular weight of an electron donor-conjugated polymer is as essential as other well-known parameters in the chemical structure of the polymer, such as length and the nature of any side groups (alkyl chains) positioned on the polymeric backbone, as well as their placement, relative strength, the ratio of the donor and acceptor moieties in the backbone of donor-acceptor (D-A)-conjugated polymers, and the arrangement of their energy levels for organic photovoltaic performance. Finding the "optimal" molecular weight for a specific conjugated polymer is an important aspect for the development of novel photovoltaic polymers. Therefore, it is evident that the chemistry of functional conjugated polymers faces major challenges and materials have to adopt a broad range of specifications in order to be established for high photovoltaic performance. In this review, the approaches followed for enhancing the molecular weight of electron-donor polymers are presented in detail, as well as how this influences the optoelectronic properties, charge transport properties, structural conformation, morphology, and the photovoltaic performance of the active layer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Grafting of molecularly imprinted polymer to porous polyethylene filtration membranes by plasma polymerization.

PubMed

Cowieson, D; Piletska, E; Moczko, E; Piletsky, S

2013-08-01

An application of plasma-induced grafting of polyethylene membranes with a thin layer of molecularly imprinted polymer (MIP) was presented. High-density polyethylene (HDPE) membranes, "Vyon," were used as a substrate for plasma grafting modification. The herbicide atrazine, one of the most popular targets of the molecular imprinting, was chosen as a template. The parameters of the plasma treatment were optimized in order to achieve a good balance between polymerization and ablation processes. Modified HDPE membranes were characterized, and the presence of the grafted polymeric layer was confirmed based on the observed weight gain, pore size measurements, and infrared spectrometry. Since there was no significant change in the porosity of the modified membranes, it was assumed that only a thin layer of the polymer was introduced on the surface. The experiments on the re-binding of the template atrazine to the membranes modified with MIP and blank polymers were performed. HDPE membranes which were grafted with polymer using continuous plasma polymerization demonstrated the best result which was expressed in an imprinted factor equal to 3, suggesting that molecular imprinting was successfully achieved.

Assessing value of innovative molecular diagnostic tests in the concept of predictive, preventive, and personalized medicine.

PubMed

Akhmetov, Ildar; Bubnov, Rostyslav V

2015-01-01

Molecular diagnostic tests drive the scientific and technological uplift in the field of predictive, preventive, and personalized medicine offering invaluable clinical and socioeconomic benefits to the key stakeholders. Although the results of diagnostic tests are immensely influential, molecular diagnostic tests (MDx) are still grudgingly reimbursed by payers and amount for less than 5 % of the overall healthcare costs. This paper aims at defining the value of molecular diagnostic test and outlining the most important components of "value" from miscellaneous assessment frameworks, which go beyond accuracy and feasibility and impact the clinical adoption, informing healthcare resource allocation decisions. The authors suggest that the industry should facilitate discussions with various stakeholders throughout the entire assessment process in order to arrive at a consensus about the depth of evidence required for positive marketing authorization or reimbursement decisions. In light of the evolving "value-based healthcare" delivery practices, it is also recommended to account for social and ethical parameters of value, since these are anticipated to become as critical for reimbursement decisions and test acceptance as economic and clinical criteria.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

PubMed

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

PubMed Central

Sing-Long, Carlos A.

2017-01-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates. PMID:28989618

Free energy landscape and molecular pathways of gas hydrate nucleation

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

Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage ordermore » parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.« less

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

DOE PAGES

Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.

2017-06-19

Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less

Evaporation of liquid droplets of nano- and micro-meter size as a function of molecular mass and intermolecular interactions: experiments and molecular dynamics simulations.

PubMed

Hołyst, Robert; Litniewski, Marek; Jakubczyk, Daniel

2017-09-13

Transport of heat to the surface of a liquid is a limiting step in the evaporation of liquids into an inert gas. Molecular dynamics (MD) simulations of a two component Lennard-Jones (LJ) fluid revealed two modes of energy transport from a vapour to an interface of an evaporating droplet of liquid. Heat is transported according to the equation of temperature diffusion, far from the droplet of radius R. The heat flux, in this region, is proportional to temperature gradient and heat conductivity in the vapour. However at some distance from the interface, Aλ, (where λ is the mean free path in the gas), the temperature has a discontinuity and heat is transported ballistically i.e. by direct individual collisions of gas molecules with the interface. This ballistic transport reduces the heat flux (and consequently the mass flux) by the factor R/(R + Aλ) in comparison to the flux obtained from temperature diffusion. Thus it slows down the evaporation of droplets of sizes R ∼ Aλ and smaller (practically for sizes from 10 3 nm down to 1 nm). We analyzed parameter A as a function of interactions between molecules and their masses. The rescaled parameter, A(k B T b /ε 11 ) 1/2 , is a linear function of the ratio of the molecular mass of the liquid molecules to the molecular mass of the gas molecules, m 1 /m 2 (for a series of chemically similar compounds). Here ε 11 is the interaction parameter between molecules in the liquid (proportional to the enthalpy of evaporation) and T b is the temperature of the gas in the bulk. We tested the predictions of MD simulations in experiments performed on droplets of ethylene glycol, diethylene glycol, triethylene glycol and tetraethylene glycol. They were suspended in an electrodynamic trap and evaporated into dry nitrogen gas. A changes from ∼1 (for ethylene glycol) to approximately 10 (for tetraethylene glycol) and has the same dependence on molecular parameters as obtained for the LJ fluid in MD simulations. The value of x = A(k B T b /ε 11 ) 1/2 is of the order of 1 (for water x = 1.8, glycerol x = 1, ethylene glycol x = 0.4, tetraethylene glycol x = 2.1 evaporating into dry nitrogen at room temperature and for Lennard-Jones fluids x = 2 for m 1 /m 2 = 1 and low temperature).

Molecular basis of quantitative structure-properties relationships (QSPR): a quantum similarity approach.

PubMed

Ponec, R; Amat, L; Carbó-Dorca, R

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett sigma constants and the logarithm of the octanol-water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Molecular basis of quantitative structure-properties relationships (QSPR): A quantum similarity approach

NASA Astrophysics Data System (ADS)

Ponec, Robert; Amat, Lluís; Carbó-dorca, Ramon

1999-05-01

Since the dawn of quantitative structure-properties relationships (QSPR), empirical parameters related to structural, electronic and hydrophobic molecular properties have been used as molecular descriptors to determine such relationships. Among all these parameters, Hammett σ constants and the logarithm of the octanol- water partition coefficient, log P, have been massively employed in QSPR studies. In the present paper, a new molecular descriptor, based on quantum similarity measures (QSM), is proposed as a general substitute of these empirical parameters. This work continues previous analyses related to the use of QSM to QSPR, introducing molecular quantum self-similarity measures (MQS-SM) as a single working parameter in some cases. The use of MQS-SM as a molecular descriptor is first confirmed from the correlation with the aforementioned empirical parameters. The Hammett equation has been examined using MQS-SM for a series of substituted carboxylic acids. Then, for a series of aliphatic alcohols and acetic acid esters, log P values have been correlated with the self-similarity measure between density functions in water and octanol of a given molecule. And finally, some examples and applications of MQS-SM to determine QSAR are presented. In all studied cases MQS-SM appeared to be excellent molecular descriptors usable in general QSPR applications of chemical interest.

Adsorbed molecules in external fields: Effect of confining potential

NASA Astrophysics Data System (ADS)

Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

2016-12-01

We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials.

Cyanide and isocyanide abundances in the cold, dark cloud TMC-1

NASA Technical Reports Server (NTRS)

Irvine, W. M.; Schloerb, F. P.

1984-01-01

Cold, dark molecular clouds are particularly useful for the study of interstellar chemistry because their physical parameters are better understood than those of heterogeneous, complex giant molecular clouds. Another advantage is their relatively small distance from the solar system. The present investigaation has the objective to provide accurate abundance ratios for several cyanides and isocyanides in order to constrain models of dark cloud chemistry. The relative abundances of such related species can be particularly useful for the study of chemical processes. The cloud TMC-1 considered in the current study has a remarkably high abundance of acetylene and polyacetylene derivatives. Data at 3 mm, corresponding to the J = 1 to 0 transitions of HCN, H(C-13)N, HN(C-13), HC(N-15), and H(N-15)C were obtained.

Exploring JWST's Capability to Constrain Habitability on Simulated Terrestrial TESS Planets

NASA Astrophysics Data System (ADS)

Tremblay, Luke; Britt, Amber; Batalha, Natasha; Schwieterman, Edward; Arney, Giada; Domagal-Goldman, Shawn; Mandell, Avi; Planetary Systems Laboratory; Virtual Planetary Laboratory

2017-01-01

In the following, we have worked to develop a flexible "observability" scale of biologically relevant molecules in the atmospheres of newly discovered exoplanets for the instruments aboard NASA's next flagship mission, the James Webb Space Telescope (JWST). We sought to create such a scale in order to provide the community with a tool with which to optimize target selection for JWST observations based on detections of the upcoming Transiting Exoplanet Satellite Survey (TESS). Current literature has laid the groundwork for defining both biologically relevant molecules as well as what characteristics would make a new world "habitable", but it has so far lacked a cohesive analysis of JWST's capabilities to observe these molecules in exoplanet atmospheres and thereby constrain habitability. In developing our Observability Scale, we utilized a range of hypothetical planets (over planetary radii and stellar insolation) and generated three self-consistent atmospheric models (of dierent molecular compositions) for each of our simulated planets. With these planets and their corresponding atmospheres, we utilized the most accurate JWST instrument simulator, created specically to process transiting exoplanet spectra. Through careful analysis of these simulated outputs, we were able to determine the relevant parameters that effected JWST's ability to constrain each individual molecular bands with statistical accuracy and therefore generate a scale based on those key parameters. As a preliminary test of our Observability Scale, we have also applied it to the list of TESS candidate stars in order to determine JWST's observational capabilities for any soon-to-be-detected planet in those solar systems.

Free energy simulations of amylin I26P mutation in a lipid bilayer.

PubMed

Jalili, Seifollah; Maleki, Afsaneh; Akhavan, Mojdeh; Najafi, Bijan; Schofield, Jeremy

2015-02-01

The amylin peptide in a dioleoylphosphatidylcholine (DOPC) bilayer is studied using united atom molecular dynamics (MD) simulations. Dynamics and transport properties of the peptide and the phospholipid bilayer are investigated. The lateral diffusion of DOPC is in the order of 10(-8) cm(2) s(-1), which is in agreement with the experimental results. The order parameter and density profile for phospholipid molecules in the bilayer are calculated. The secondary structure of amylin peptide shows that the amino acids in two terminals are structureless and two α-helical segments in the peptide are connected through an unstructured link. This structure is similar to the experimental structure in the membrane-mimicking media. Free energy calculations of the Ile26 → Pro mutation in the amylin peptide are performed in the bilayer and in aqueous solution using molecular dynamics simulations and a thermodynamic cycle. It is shown that in the mutated peptide in aqueous solution, the α-helix structure changes to a 5-helix, whereas this configuration is preserved in the bilayer environment. It is interesting that the accessible surface area increases for hydrophobic residues in the bilayer and for hydrophilic residues in aqueous solution as the coupling parameter changes from 0 to 1. These results are significant to understanding the aggregation mechanism of human amylin monomers in membranes to the dimers, trimers, oligomers, and fibrils associated with the type 2 diabetes at the atomic level.

Evaluation of various molecular parameters as predictors of bioconcentration in fish

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

Connell, D.W.; Schueuermann G3

1988-06-01

A reliable set of data on the bioconcentration factors (KB) of a diverse range of compounds in fish was selected from the literature. Using the structures of these compounds, the following molecular parameters were calculated: molecular weight (MW), solvent accessible molecular surface area (SASA), solvent accessible molecular volume (SAV), molar refraction (MR), largest principal moment of inertia (LPMI) and several molecular connectivity indices of the Randic type (1 chi, 2 chi, 3 chi, 1 chi vr, 3 chi c). The relationships between these parameters and log KB were evaluated for all compounds and the following subgroups: chlorinated hydrocarbons (CHC), polyaromaticmore » hydrocarbons (PAH), and CHC and PAH combined. These relationships indicated that SASA, SAV, and MR were good predictors of log KB for the CHC and PAH combined or alone and the other parameters were less satisfactory with these groups. In addition with the CHC, the log of these parameters displayed an improved correlation with log KB due to apparent nonlinearity in the log to linear relationship. Thus, with these groups of compounds, calculated values of SASA, SAV, and MR provide a satisfactory means of estimating log KB without measured data.« less

Quantum Chemically Estimated Abraham Solute Parameters Using Multiple Solvent-Water Partition Coefficients and Molecular Polarizability.

PubMed

Liang, Yuzhen; Xiong, Ruichang; Sandler, Stanley I; Di Toro, Dominic M

2017-09-05

Polyparameter Linear Free Energy Relationships (pp-LFERs), also called Linear Solvation Energy Relationships (LSERs), are used to predict many environmentally significant properties of chemicals. A method is presented for computing the necessary chemical parameters, the Abraham parameters (AP), used by many pp-LFERs. It employs quantum chemical calculations and uses only the chemical's molecular structure. The method computes the Abraham E parameter using density functional theory computed molecular polarizability and the Clausius-Mossotti equation relating the index refraction to the molecular polarizability, estimates the Abraham V as the COSMO calculated molecular volume, and computes the remaining AP S, A, and B jointly with a multiple linear regression using sixty-five solvent-water partition coefficients computed using the quantum mechanical COSMO-SAC solvation model. These solute parameters, referred to as Quantum Chemically estimated Abraham Parameters (QCAP), are further adjusted by fitting to experimentally based APs using QCAP parameters as the independent variables so that they are compatible with existing Abraham pp-LFERs. QCAP and adjusted QCAP for 1827 neutral chemicals are included. For 24 solvent-water systems including octanol-water, predicted log solvent-water partition coefficients using adjusted QCAP have the smallest root-mean-square errors (RMSEs, 0.314-0.602) compared to predictions made using APs estimated using the molecular fragment based method ABSOLV (0.45-0.716). For munition and munition-like compounds, adjusted QCAP has much lower RMSE (0.860) than does ABSOLV (4.45) which essentially fails for these compounds.

Theoretical estimation of mesogenic characteristics of 4-methyl (2‧-hydroxy,4‧-n-hexadecyloxy) azobenzene - a nematic liquid crystal

NASA Astrophysics Data System (ADS)

Gaurav, Pankaj Kumar; Roychoudhury, Mihir

2014-03-01

The compound 4-methyl (2‧-hydroxy,4‧-n-hexadecyloxy) azobenzene was synthesized by Prajapati and co-workers (Mol. Cryst. Liq. Cryst. 369 (2001), pp. 37-46). Subsequent experiments (D. Pal, [PhD thesis], University of Lucknow, Lucknow, India, 2007) confirmed that the compound exists in nematic phase for a small range of temperature (72°C-80°C). In the present work, optimization of molecular geometry has been carried out by employing the Gaussian 03 suit of programs without any constraint using density functional B3LYP along with 6-31G** basis set and checked for imaginary frequencies. A detailed investigation on intermolecular interaction energy at various interacting configurations has been carried out. In order to study the mesogenic characteristics of the molecule, an attempt has been made to estimate the variation of order parameter with respect to the change in temperature as well as degrees of freedom. These studies will be helpful to understanding the mesogenic character of any molecule prior to synthesis and promises future application in molecular engineering.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Grillo, Damián A.; Albano, Juan M. R.; Mocskos, Esteban E.; Facelli, Julio C.; Pickholz, Mónica; Ferraro, Marta B.

2018-06-01

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

A mathematical approach to molecular organization and proteolytic disintegration of bacterial inclusion bodies.

PubMed

Cubarsi, R; Carrió, M M; Villaverde, A

2005-09-01

The in vivo proteolytic digestion of bacterial inclusion bodies (IBs) and the kinetic analysis of the resulting protein fragments is an interesting approach to investigate the molecular organization of these unconventional protein aggregates. In this work, we describe a set of mathematical instruments useful for such analysis and interpretation of observed data. These methods combine numerical estimation of digestion rate and approximation of its high-order derivatives, modelling of fragmentation events from a mixture of Poisson processes associated with differentiated protein species, differential equations techniques in order to estimate the mixture parameters, an iterative predictor-corrector algorithm for describing the flow diagram along the cascade process, as well as least squares procedures with minimum variance estimates. The models are formulated and compared with data, and successively refined to better match experimental observations. By applying such procedures as well as newer improved algorithms of formerly developed equations, it has been possible to model, for two kinds of bacterially produced aggregation prone recombinant proteins, their cascade digestion process that has revealed intriguing features of the IB-forming polypeptides.

Mechanical properties of drug loaded diblock copolymer bilayers: A molecular dynamics study.

PubMed

Grillo, Damián A; Albano, Juan M R; Mocskos, Esteban E; Facelli, Julio C; Pickholz, Mónica; Ferraro, Marta B

2018-06-07

In this work, we present results of coarse-grained simulations to study the encapsulation of prilocaine (PLC), both neutral and protonated, on copolymer bilayers through molecular dynamics simulations. Using a previously validated membrane model, we have simulated loaded bilayers at different drug concentrations and at low (protonated PLC) and high (neutral PLC) pH levels. We have characterized key structural parameters of the loaded bilayers in order to understand the effects of encapsulation of PLC on the bilayer structure and mechanical properties. Neutral PLC was encapsulated in the hydrophobic region leading to a thickness increase, while the protonated species partitioned between the water phase and the poly(ethylene oxide)-poly(butadiene) (PBD) interface, relaxing the PBD region and leading to a decrease in the thickness. The tangential pressures of the studied systems were calculated, and their components were decomposed in order to gain insights on their compensation. In all cases, it is observed that the loading of the membrane does not significantly decrease the stability of the bilayer, indicating that the system could be used for drug delivery.

Fluorescence molecular tomography reconstruction via discrete cosine transform-based regularization

NASA Astrophysics Data System (ADS)

Shi, Junwei; Liu, Fei; Zhang, Jiulou; Luo, Jianwen; Bai, Jing

2015-05-01

Fluorescence molecular tomography (FMT) as a noninvasive imaging modality has been widely used for biomedical preclinical applications. However, FMT reconstruction suffers from severe ill-posedness, especially when a limited number of projections are used. In order to improve the quality of FMT reconstruction results, a discrete cosine transform (DCT) based reweighted L1-norm regularization algorithm is proposed. In each iteration of the reconstruction process, different reweighted regularization parameters are adaptively assigned according to the values of DCT coefficients to suppress the reconstruction noise. In addition, the permission region of the reconstructed fluorophores is adaptively constructed to increase the convergence speed. In order to evaluate the performance of the proposed algorithm, physical phantom and in vivo mouse experiments with a limited number of projections are carried out. For comparison, different L1-norm regularization strategies are employed. By quantifying the signal-to-noise ratio (SNR) of the reconstruction results in the phantom and in vivo mouse experiments with four projections, the proposed DCT-based reweighted L1-norm regularization shows higher SNR than other L1-norm regularizations employed in this work.

Orientation dynamics in isotropic phases of model oligofluorenes: glass or liquid crystal.

PubMed

Somma, E; Chi, C; Loppinet, B; Grinshtein, J; Graf, R; Fytas, G; Spiess, H W; Wegner, G

2006-05-28

Orientation molecular dynamics were investigated in a series of "defect-free" oligofluorenes by depolarized dynamic light scattering and dynamic NMR spectroscopy. Typical liquid crystalline pretransitional dynamics were observed upon cooling the isotropic phase to the liquid crystalline phase with strong increase of the scattered intensity and slowing down of the characteristic time of the probed collective relaxation. This is well accounted for by the Landau-de Gennes theory, however, with a strong temperature dependence of the viscosity coefficient, reflecting the proximity of the glass transition. For the trimer the two transitions almost overlap and the molecular orientation coincide with the alpha-relaxation associated with the glass transition. The NMR measurements confirm that the time scale of the dynamics is completely governed by the glass process, yet the geometry of the motion is anisotropic, yielding order parameters ranging from 0.15 to 0.25 for the long axis in the liquid crystalline phase. The glass transition is therefore geometrically restricted with poorly ordered mesophase which is consistent with the weak transverse phonons in the light scattering experiment down to Tg+20 K.

Spectroscopic investigation on the efficient organic nonlinear crystals of pure and diethanolamine added DAST.

PubMed

Karthikeyan, C; Haja Hameed, A S; Sagaya Agnes Nisha, J; Ravi, G

2013-11-01

4-N,N'-dimethylamino-N-methyl-4-stilbazolium toyslate (DAST) and diethanolamine (DEA) added DAST crystals are grown by slow cooling method. The corresponding powder samples are examined by characterization studies such as XRD, FT-IR, FT-Raman, UV-Vis-NIR and photoluminescence studies. From the powder X-ray diffraction, their lattice parameter values are found out. Since the vibrational spectra of the molecules are considerably contributed to their linear and nonlinear optical effects, Infrared and Raman spectroscopic studies are carried out for the samples. The UV-Vis-NIR absorption spectra of the samples are used to find the nature of transitions occurred in the samples. Using the density functional theory, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analyses are done in order to explain the transition and density of states (DOS). The first order hyperpolarizability is calculated by HF and B3LYP/6-311 G(d,p) basis sets for the DAST molecule. From the photoluminescence (PL) spectral studies, the strong excitation emissions are observed. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular dynamics study of the isotropic-nematic quench.

PubMed

Bradac, Z; Kralj, S; Zumer, S

2002-02-01

Effects of cylindrical and spherical confinement on the kinetics of the isotropic-nematic quench is studied numerically. The nematic liquid crystal structure was modeled by a modified induced-dipole--induced-dipole interaction. Molecules were allowed to wander around points of a hexagonal lattice. Brownian molecular dynamics was used in order to access macroscopic time scales. In the bulk we distinguish between the early, domain, and late stage regime. The early regime is characterized by the exponential growth of the nematic uniaxial order parameter. In the domain regime domains are clearly visible and the average nematic domain size xi(d) obeys the dynamical scaling law xi(d)-t(gamma). The late stage evolution is dominated by dynamics of individual defects. In a confined system the qualitative change of the scaling behavior appears when xi(d) becomes comparable to a typical linear dimension R of the confinement. In the confining regime (xi(d)>or=R) the scaling coefficient gamma depends on the details of the confinement and also the final equilibrium nematic structure. The domain growth is well described with the Kibble-Zurek mechanism.

Study of crystal-field interaction in magnetic frustrated lead pyrochlore Gd2Pb2O7

NASA Astrophysics Data System (ADS)

Swarnakar, D.; Jana, Y. M.

2018-05-01

A fine tuning between the crystal field and the molecular field to adopt unique ground state in frustrated magnetic R2M2O7 pyrochlores structures is made by the variation of chemical pressure at R-site caused by substitution of nonmagnetic cation of M-site. Existence of larger cation at M-site increases the lattice parameter or nearest-neighbor bond distance between magnetic R-spins, and causes subtle changes to the local oxygen environment surrounding each R-ion, thereby reduces the chemical pressure at R-site which leads to a dramatic change in the crystal-field and molecular field. To investigate the effect of chemical pressure, the experimental results of powder magnetic susceptibility and isothermal magnetization of the frustrated compound Gd2Pb2O7 containing largest cation, e.g. lead (Pb), at M4+-sites were simulated and analyzed employing a D3d crystal-field (CF) and anisotropic molecular field at R-sites in the self- consistent mean-field approach. The second-ordered axial parameter B20 and total CF splitting of the ground multiplet Gd-ion in Gd2Pb2O7 are 477 cm-1 and 4.8 cm-1 respectively which are the lowest among their isomorphous counterparts, implying reduced effect of the crystal-field at Gd site in Gd2Pb2O7.

Molecular structure of hybrid imino-chalcone in the solid state: X-ray diffraction, spectroscopy study and third-order nonlinear optical properties

NASA Astrophysics Data System (ADS)

Custodio, J. M. F.; Santos, F. G.; Vaz, W. F.; Cunha, C. E. P.; Silveira, R. G.; Anjos, M. M.; Campos, C. E. M.; Oliveira, G. R.; Martins, F. T.; da Silva, C. C.; Valverde, C.; Baseia, B.; Napolitano, H. B.

2018-04-01

A comprehensive structural study of the compound (2E)-1-((E)-4-(4-methoxybenzylideneamino)phenyl)-3-(4-methoxyphenyl)prop-2-en-1-one was carried out in this work. Single crystal X-ray diffraction (SCXRD), X-ray powder diffraction (XRPD), NMR, Raman and Infrared spectroscopies, and DFT calculations were performed for characterization of this iminochalcone hybrid. Intermolecular interactions were described by Hirshfeld surface analysis derived from crystal structure. Reactivity and intramolecular charge transfer were investigated using the frontier molecular orbitals and molecular electrostatic potential. In addition, we have calculated the Nonlinear Optical Properties at the CAM-B3LYP/6-311+g(d) level of theory in the presence of different solvents (gas-phase, acetone, chloroform, dichloromethane, dimethyl sulfoxide, ethanol, methanol, and water), being found meaningful NLO parameters for our compound. At last, there is a good agreement between calculated and experimental IR spectrum, allowing the assignment of some of normal vibrational modes of the iminochalcone hybrid.

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

PubMed Central

Denning, Denise; Roos, Wouter H.

2016-01-01

ABSTRACT The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a defined microenvironment has also garnered deep insight into the engineering mechanisms existing within the cell. This review presents recent experimental findings on the influence of several parameters of the extracellular environment on cell behavior and fate, such as substrate topography, stiffness, chemistry and charge. In addition, the use of synthetic environments to measure physical properties of the reconstituted cytoskeleton and their interaction with intracellular proteins such as molecular motors is discussed, which is relevant for understanding cell migration, division and structural integrity, as well as intracellular transport. Insight is provided regarding the next steps to be taken in this interdisciplinary field, in order to achieve the global aim of artificially directing cellular response. PMID:27266767

Insights into molecular structure and digestion rate of oat starch.

PubMed

Xu, Jinchuan; Kuang, Qirong; Wang, Kai; Zhou, Sumei; Wang, Shuo; Liu, Xingxun; Wang, Shujun

2017-04-01

The in vitro digestibility of oat starch and its relationship with starch molecular structure was investigated. The in vitro digestion results showed that the first-order kinetic constant (k) of oat starches (OS-1 and OS-2) was lower than that of rice starch. The size of amylose chains, amylose content and degree of branching (DB) of amylopectin in oat starch were significantly higher than the corresponding parameters in rice starch. The larger molecular size of oat starch may account for its lower digestion rate. The fine structure of amylopectin showed that oat starch had less chains of DP 6-12 and DP>36, which may explain the small difference in digestion rate between oat and rice starch. The biosynthesis model from oat amylopectin fine structure data suggested a lower starch branching enzyme (SBE) activity and/or a higher starch synthase (SS) activity, which may decrease the DB of oat starch and increase its digestion rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Investigation of oxygen self-diffusion in PuO 2 by combining molecular dynamics with thermodynamic calculations

DOE PAGES

Saltas, V.; Chroneos, A.; Cooper, Michael William D.; ...

2016-01-01

In the present work, the defect properties of oxygen self-diffusion in PuO 2 are investigated over a wide temperature (300–1900 K) and pressure (0–10 GPa) range, by combining molecular dynamics simulations and thermodynamic calculations. Based on the well-established cBΩ thermodynamic model which connects the activation Gibbs free energy of diffusion with the bulk elastic and expansion properties, various point defect parameters such as activation enthalpy, activation entropy, and activation volume were calculated as a function of T and P. Molecular dynamics calculations provided the necessary bulk properties for the proper implementation of the thermodynamic model, in the lack of anymore » relevant experimental data. The estimated compressibility and the thermal expansion coefficient of activation volume are found to be more than one order of magnitude greater than the corresponding values of the bulk plutonia. As a result, the diffusion mechanism is discussed in the context of the temperature and pressure dependence of the activation volume.« less

Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

NASA Astrophysics Data System (ADS)

Lan, Yaqi

Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

Sampling the isothermal-isobaric ensemble by Langevin dynamics

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

Gao, Xingyu; Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094; CAEP Software Center for High Performance Numerical Simulation, Huayuan Road 6, Beijing 100088

2016-03-28

We present a new method of conducting fully flexible-cell molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way, in the sense that the stationary configurational distribution is proved to be consistent with that of the isothermal-isobaric ensemble. In order to apply the proposed method in computer simulations, a second order symmetric numerical integration scheme is developed by Trotter’s splitting of the single-step propagator. Moreover, a practical guide of choosing working parameters is suggested for user specified thermo- and baro-coupling timemore » scales. The method and software implementation are carefully validated by a numerical example.« less

Crystal structure of a new alpha-cyclodextrin hydrate form. Molecular geometry and packing features: disordered solvent contribution.

PubMed

Puliti, R; Mattia, C A; Paduano, L

1998-08-01

The crystallographic study of a new hydrated form of alpha-cyclodextrin (cyclohexaamylose) is reported. C36H60O30 . 11H2O; space group P2(1)2(1)2(1) with cell constants a = 13.839(3), b = 15.398(3), c = 24.209(7) A; final discrepancy index R = 0.057 for the 5182 observed reflections and 632 refined parameters. Besides four ordered water molecules placed outside alpha-cyclodextrins, the structure shows regions of severely disordered solvent mainly confined in the oligosaccharide cavities. The contribution of the observed disorder has been computed via Fourier inversions of the residual electron density and incorporated into the structure factors in further refinements of the ordered part. The alpha-cyclodextrin molecule assumes a relaxed round shape stabilised by a ring sequence of all the six possible O2 ... O3 intramolecular hydrogen bonds. The four ordered water molecules take part in an extensive network of hydrogen bonds (infinite chains and loops) without modifying the scheme of intramolecular H-bonds or the (-)gauche conformation of O-6-H hydroxyl groups. The structure shows a new molecular arrangement, for an "empty" hydrated alpha-cyclodextrin, like that "brick-type" observed for alpha-CD in the iodoanilide trihydrate complex crystallising in an isomorphous cell.

Molecular dynamics simulation of geminal dicationic ionic liquids [Cn(mim)2][NTf2]2 - structural and dynamical properties.

PubMed

Moosavi, Majid; Khashei, Fatemeh; Sedghamiz, Elaheh

2017-12-20

In this work, the structural and dynamical properties of two imidazolium-based geminal dicationic ionic liquids (GDILs), i.e. [C n (mim) 2 ][NTf 2 ] 2 with n = 3 and 5, have been studied to obtain a fundamental understanding of the molecular basis of the macroscopic and microscopic properties of the bulk liquid phase. To achieve this purpose, molecular dynamics (MD) simulation, density functional theory (DFT) and atoms in molecule (AIM) methods were used. Interaction energies, charge transfers and hydrogen bonds between the cation and anions of each studied GDIL were investigated by DFT calculations and also AIM. The mean square displacement (MSD), self-diffusion coefficient, and transference number of the cation and anions, and also the density, viscosity and electrical conductivity of the studied GDILs, were computed at 333.15 K and at 1 atm. The simulated values were in good agreement with the experimental data. The effect of linkage alkyl chain length on the thermodynamic, transport and structural properties of these GDILs has been investigated. The structural features of these GDILs were characterized by calculating the partial site-site radial distribution functions (RDFs) and spatial distribution functions (SDFs). The heterogeneity order parameter (HOP) has been used to describe the spatial structures of these GDILs and the distribution of the angles formed between two cation heads and the middle carbon atom of the linkage alkyl chain was analyzed in these ILs. To investigate the temporal heterogeneity of the studied GDILs, the deviation of the self-part of the van Hove correlation function, G s (r[combining right harpoon above],t), from the Gaussian distribution of particle displacement and also the second-order non-Gaussian parameter, α 2 (t), were used. Since, the transport and interfacial properties and ionic characteristics of these GDILs were studied experimentally in our previous studies as a function of linkage chain length and temperature, in this work, we try to give a better perspective of the structure and dynamics of these systems at a molecular level.

Epitope mapping of monoclonal antibody HPT-101: a study combining dynamic force spectroscopy, ELISA and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Stangner, Tim; Angioletti-Uberti, Stefano; Knappe, Daniel; Singer, David; Wagner, Carolin; Hoffmann, Ralf; Kremer, Friedrich

2015-12-01

By combining enzyme-linked immunosorbent assay (ELISA) and optical tweezers-assisted dynamic force spectroscopy (DFS), we identify for the first time the binding epitope of the phosphorylation-specific monoclonal antibody (mAb) HPT-101 to the Alzheimer's disease relevant peptide tau[pThr231/pSer235] on the level of single amino acids. In particular, seven tau isoforms are synthesized by replacing binding relevant amino acids by a neutral alanine (alanine scanning). From the binding between mAb HPT-101 and the alanine-scan derivatives, we extract specific binding parameters such as bond lifetime {τ }0, binding length {x}{ts}, free energy of activation {{Δ }}G (DFS) and affinity constant {K}{{a}} (ELISA, DFS). Based on these quantities, we propose criteria to identify essential, secondary and non-essential amino acids, being representative of the antibody binding epitope. The obtained results are found to be in full accord for both experimental techniques. In order to elucidate the microscopic origin of the change in binding parameters, we perform molecular dynamics (MD) simulations of the free epitope in solution for both its parent and modified form. By taking the end-to-end distance {d}{{E}-{{E}}} and the distance between the α-carbons {d}{{C}-{{C}}} of the phosphorylated residues as gauging parameters, we measure how the structure of the epitope depends on the type of substitution. In particular, whereas {d}{{C}-{{C}}} is sometimes conserved between the parent and modified form, {d}{{E}-{{E}}} strongly changes depending on the type of substitution, correlating well with the experimental data. These results are highly significant, offering a detailed microscopic picture of molecular recognition.

Translational, rotational and internal dynamics of amyloid β-peptides (Aβ40 and Aβ42) from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Bora, Ram Prasad; Prabhakar, Rajeev

2009-10-01

In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid-β peptides Aβ40 and Aβ42 have been calculated from 150 ns molecular dynamics simulations in aqueous solution. The computed parameters have been compared with the experimentally measured values. The calculated DT of 1.61×10-6 cm2/s and 1.43×10-6 cm2/s for Aβ40 and Aβ42, respectively, at 300 K was found to follow the correct trend defined by the Debye-Stokes-Einstein relation that its value should decrease with the increase in the molecular weight. The estimated DR for Aβ40 and Aβ42 at 300 K are 0.085 and 0.071 ns-1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of Aβ40 and Aβ42 were observed to decay at nano- and picosecond time scales, respectively. The significantly different time decays of these functions validate the factorization of the total correlation function (Ctot(t)) of Aβ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both Aβ40 and Aβ42. In addition, an effective rotational correlation time of Aβ40 is also computed at 18 °C and the computed value (2.30 ns) is in close agreement with the experimental value of 2.45 ns. The computed S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of Aβ40 and Aβ42 are in accord with the previous studies.

Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

PubMed

Dracínský, Martin; Kaminský, Jakub; Bour, Petr

2009-03-07

Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in future quantum chemistry packages is desirable.

Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors.

PubMed

Duardo-Sánchez, Aliuska; Munteanu, Cristian R; Riera-Fernández, Pablo; López-Díaz, Antonio; Pazos, Alejandro; González-Díaz, Humberto

2014-01-27

The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order k(th) (W(k)). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the W(k)(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated W(k)(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation).

Spectral studies of 2-pyrazoline derivatives: structural elucidation through single crystal XRD and DFT calculations.

PubMed

Chinnaraja, D; Rajalakshmi, R; Srinivasan, T; Velmurugan, D; Jayabharathi, J

2014-04-24

A series of biologically active N-thiocarbamoyl pyrazoline derivatives have been synthesized using anhydrous potassium carbonate as the catalyst. All the synthesized compounds were characterized by FT-IR, (1)H NMR, (13)C NMR spectral studies, LCMS, CHN Analysis and X-ray diffraction analysis (compound 7). In order to supplement the XRD parameters, molecular modelling was carried out by Gaussian 03W. From the optimized structure, the energy, dipolemoment and HOMO-LUMO energies of all the systems were calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiscale Analysis of Structurally-Graded Microstructures Using Molecular Dynamics, Discrete Dislocation Dynamics and Continuum Crystal Plasticity

NASA Technical Reports Server (NTRS)

Saether, Erik; Hochhalter, Jacob D.; Glaessgen, Edward H.; Mishin, Yuri

2014-01-01

A multiscale modeling methodology is developed for structurally-graded material microstructures. Molecular dynamic (MD) simulations are performed at the nanoscale to determine fundamental failure mechanisms and quantify material constitutive parameters. These parameters are used to calibrate material processes at the mesoscale using discrete dislocation dynamics (DD). Different grain boundary interactions with dislocations are analyzed using DD to predict grain-size dependent stress-strain behavior. These relationships are mapped into crystal plasticity (CP) parameters to develop a computationally efficient finite element-based DD/CP model for continuum-level simulations and complete the multiscale analysis by predicting the behavior of macroscopic physical specimens. The present analysis is focused on simulating the behavior of a graded microstructure in which grain sizes are on the order of nanometers in the exterior region and transition to larger, multi-micron size in the interior domain. This microstructural configuration has been shown to offer improved mechanical properties over homogeneous coarse-grained materials by increasing yield stress while maintaining ductility. Various mesoscopic polycrystal models of structurally-graded microstructures are generated, analyzed and used as a benchmark for comparison between multiscale DD/CP model and DD predictions. A final series of simulations utilize the DD/CP analysis method exclusively to study macroscopic models that cannot be analyzed by MD or DD methods alone due to the model size.

Probing numerical Laplace inversion methods for two and three-site molecular exchange between interconnected pore structures.

PubMed

Silletta, Emilia V; Franzoni, María B; Monti, Gustavo A; Acosta, Rodolfo H

2018-01-01

Two-dimension (2D) Nuclear Magnetic Resonance relaxometry experiments are a powerful tool extensively used to probe the interaction among different pore structures, mostly in inorganic systems. The analysis of the collected experimental data generally consists of a 2D numerical inversion of time-domain data where T 2 -T 2 maps are generated. Through the years, different algorithms for the numerical inversion have been proposed. In this paper, two different algorithms for numerical inversion are tested and compared under different conditions of exchange dynamics; the method based on Butler-Reeds-Dawson (BRD) algorithm and the fast-iterative shrinkage-thresholding algorithm (FISTA) method. By constructing a theoretical model, the algorithms were tested for a two- and three-site porous media, varying the exchange rates parameters, the pore sizes and the signal to noise ratio. In order to test the methods under realistic experimental conditions, a challenging organic system was chosen. The molecular exchange rates of water confined in hierarchical porous polymeric networks were obtained, for a two- and three-site porous media. Data processed with the BRD method was found to be accurate only under certain conditions of the exchange parameters, while data processed with the FISTA method is precise for all the studied parameters, except when SNR conditions are extreme. Copyright © 2017 Elsevier Inc. All rights reserved.

Phase diagram and universality of the Lennard-Jones gas-liquid system.

PubMed

Watanabe, Hiroshi; Ito, Nobuyasu; Hu, Chin-Kun

2012-05-28

The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class.

Calcium environment in silicate and aluminosilicate glasses probed by ⁴³Ca MQMAS NMR experiments and MD-GIPAW calculations.

PubMed

Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Florian, Pierre; Charpentier, Thibault

2015-01-01

⁴³Ca MQMAS NMR spectra of three silica-based glasses in which Ca²⁺ ions play different structural roles have been collected and processed in order to extract the underlying NMR parameter distributions. The NMR parameters have been interpreted with the help of molecular dynamics simulations and DFT-GIPAW calculations. This synergetic experimental-computational approach has allowed us to investigate the Ca environment, to estimate Ca coordination numbers from MD-derived models, and to push further the discussion about ⁴³Ca NMR sensitivity to the first and second coordination spheres: ⁴³Ca δiso and Ca-O distance can be successfully correlated as a function of Ca coordination number. Copyright © 2015 Elsevier Inc. All rights reserved.

Review of concepts useful for maintaining quality of male reproductive field samples for laboratory study

USGS Publications Warehouse

Jenkins, Jill A.

2011-01-01

Investigations into cellular and molecular characteristics of male gametes obtained from fish in natural ecosystems require careful sample handling and shipping in order to minimize artifacts. Maintaining sample integrity engenders confident assessments of ecosystem health, whereby animal condition is often reflected by gamete biomarkers - indicators that respond in measurable ways to changes. A number of our investigations have addressed the hypothesis that biomarkers from fish along a pollution gradient are reflective of site location. Species biology and the selected biological endpoints direct choice of parameters such as: temperature, buffer osmolality, time in transit, fixation, cryoprotectants, protease inhibition, and antibiotic inclusion in extender. This paper will highlight case studies, and outline parameters and thoughts on approaches for use by field and laboratory researchers.

Enantiodiscrimination of flexible cyclic solutes using NMR spectroscopy in polypeptide chiral mesophases: investigation of cis-decalin and THF.

PubMed

Aroulanda, Christie; Lafon, Olivier; Lesot, Philippe

2009-08-06

The conformational dynamics and orientational behavior of two model cyclic molecules, cis-decalin (cis-dec) and tetrahydrofurane (THF), dissolved in weakly ordering, polypeptidic chiral liquid crystals (CLCs) are theoretically discussed and experimentally investigated using deuterium and carbon-13 NMR spectroscopies. The analysis of enantiomeric and enantiotopic discriminations in these compounds is shown to depend on the rate of conformational exchange regime, slow or fast. The slow exchange regime is illustrated through the case of cis-dec at low temperature (243 K). We show that the deuterium NMR spectra in this regime can be qualitatively and quantitatively interpreted by restricting the conformational pathway of cis-dec to two enantiomeric conformers of C(2)-symmetry. The orientational order parameters of these interconverting enantiomers are calculated by matching the (2)H quadrupolar splittings with calculated conformer structures. The fast exchange regime is investigated through the examples of cis-dec at high temperature (356 K) and THF at room temperature (300 K). The (2)H NMR spectra above the coalescence temperature are analyzed by introducing the concept of "average molecular structure". This fictitious structure allows easily identifying NMR equivalences of solutes dissolved in CLC. However, it cannot be applied to determine consistent orientational order parameters. This study emphasizes that enantiotopic discriminations observed for flexible molecules in the fast exchange regime can be quantitatively interpreted only by considering the orientational order of each conformer.

Uncertainty quantification and propagation of errors of the Lennard-Jones 12-6 parameters for n-alkanes

PubMed Central

Knotts, Thomas A.

2017-01-01

Molecular simulation has the ability to predict various physical properties that are difficult to obtain experimentally. For example, we implement molecular simulation to predict the critical constants (i.e., critical temperature, critical density, critical pressure, and critical compressibility factor) for large n-alkanes that thermally decompose experimentally (as large as C48). Historically, molecular simulation has been viewed as a tool that is limited to providing qualitative insight. One key reason for this perceived weakness in molecular simulation is the difficulty to quantify the uncertainty in the results. This is because molecular simulations have many sources of uncertainty that propagate and are difficult to quantify. We investigate one of the most important sources of uncertainty, namely, the intermolecular force field parameters. Specifically, we quantify the uncertainty in the Lennard-Jones (LJ) 12-6 parameters for the CH4, CH3, and CH2 united-atom interaction sites. We then demonstrate how the uncertainties in the parameters lead to uncertainties in the saturated liquid density and critical constant values obtained from Gibbs Ensemble Monte Carlo simulation. Our results suggest that the uncertainties attributed to the LJ 12-6 parameters are small enough that quantitatively useful estimates of the saturated liquid density and the critical constants can be obtained from molecular simulation. PMID:28527455

Oxyfluorfen toxic effect on S. obliquus evaluated by different photosynthetic and enzymatic biomarkers.

PubMed

Geoffroy, L; Dewez, D; Vernet, G; Popovic, R

2003-11-01

The effect of oxyfluorfen was investigated when alga Scenedesmus obliquus has been exposed to different concentrations (7.5, 15, and 22.5 microg x L(-1)) at 12, 24, and 48 hours of exposure. Toxicity test was done by using 13 biomarkers concerning growth rate, chlorophyll content and indicators of photosynthetic and antioxidant enzyme activities. The change of the 13 parameters showed a great variation of sensitivity indicating differences in parameters' suitability to be used as biomarkers when alga culture was exposed to oxyfluorfen toxicity. The order of sensitivity between those biomarkers was: Antenna size (ABS/RC) > Chlorophyll content > Catalase (CAT) > Operational PSII quantum yield (phiS(PSII)) > Glutathione S-transferase (GST) > Functional plastoquinone pool (Q(PQ)) > Glutathione reductase (GR) > Growth rate > Nonphotochemical quenching (QN) > Proton gradient quenching (Q(Emax)) > Ascorbate peroxidase (APX) > Photochemical quenching (Q(p)) > Maximum PSII quantum yield (Phi(PSII)). The effect of oxyfluorfen on the changes of those parameters was interpreted as a result of herbicide mode of action at molecular level of alga cellular system. This study indicated for some photosynthetic and enzymatic biomarkers to be useful indicators of toxicity effect induced in non-target alga species. Determination of biomarkers' sensitivity order may facilitate their selection to be used in environmental risk assessment of polluted water.

Electro-optical parameters of bond polarizability model for aluminosilicates.

PubMed

Smirnov, Konstantin S; Bougeard, Daniel; Tandon, Poonam

2006-04-06

Electro-optical parameters (EOPs) of bond polarizability model (BPM) for aluminosilicate structures were derived from quantum-chemical DFT calculations of molecular models. The tensor of molecular polarizability and the derivatives of the tensor with respect to the bond length are well reproduced with the BPM, and the EOPs obtained are in a fair agreement with available experimental data. The parameters derived were found to be transferable to larger molecules. This finding suggests that the procedure used can be applied to systems with partially ionic chemical bonds. The transferability of the parameters to periodic systems was tested in molecular dynamics simulation of the polarized Raman spectra of alpha-quartz. It appeared that the molecular Si-O bond EOPs failed to reproduce the intensity of peaks in the spectra. This limitation is due to large values of the longitudinal components of the bond polarizability and its derivative found in the molecular calculations as compared to those obtained from periodic DFT calculations of crystalline silica polymorphs by Umari et al. (Phys. Rev. B 2001, 63, 094305). It is supposed that the electric field of the solid is responsible for the difference of the parameters. Nevertheless, the EOPs obtained can be used as an initial set of parameters for calculations of polarizability related characteristics of relevant systems in the framework of BPM.

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation

NASA Astrophysics Data System (ADS)

Hudson, Brian D.; George, Ashley R.; Ford, Martyn G.; Livingstone, David J.

1992-04-01

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Comparing and Correlating Solubility Parameters Governing the Self-Assembly of Molecular Gels Using 1,3:2,4-Dibenzylidene Sorbitol as the Gelator

PubMed Central

2014-01-01

Solvent properties play a central role in mediating the aggregation and self-assembly of molecular gelators and their growth into fibers. Numerous attempts have been made to correlate the solubility parameters of solvents and gelation abilities of molecular gelators, but a comprehensive comparison of the most important parameters has yet to appear. Here, the degree to which partition coefficients (log P), Henry’s law constants (HLC), dipole moments, static relative permittivities (εr), solvatochromic ET(30) parameters, Kamlet–Taft parameters (β, α, and π), Catalan’s solvatochromic parameters (SPP, SB, and SA), Hildebrand solubility parameters (δi), and Hansen solubility parameters (δp, δd, δh) and the associated Hansen distance (Rij) of 62 solvents (covering a wide range of properties) can be correlated with the self-assembly and gelation of 1,3:2,4-dibenzylidene sorbitol (DBS) gelation, a classic molecular gelator, is assessed systematically. The approach presented describes the basis for each of the parameters and how it can be applied. As such, it is an instructional blueprint for how to assess the appropriate type of solvent parameter for use with other molecular gelators as well as with molecules forming other types of self-assembled materials. The results also reveal several important insights into the factors favoring the gelation of solvents by DBS. The ability of a solvent to accept or donate a hydrogen bond is much more important than solvent polarity in determining whether mixtures with DBS become solutions, clear gels, or opaque gels. Thermodynamically derived parameters could not be correlated to the physical properties of the molecular gels unless they were dissected into their individual HSPs. The DBS solvent phases tend to cluster in regions of Hansen space and are highly influenced by the hydrogen-bonding HSP, δh. It is also found that the fate of this molecular gelator, unlike that of polymers, is influenced not only by the magnitude of the distance between the HSPs for DBS and the HSPs of the solvent, Rij, but also by the directionality of Rij: if the solvent has a larger hydrogen-bonding HSP (indicating stronger H-bonding) than that of the DBS, then clear gels are formed; opaque gels form when the solvent has a lower δh than does DBS. PMID:24849281

Comparing and correlating solubility parameters governing the self-assembly of molecular gels using 1,3:2,4-dibenzylidene sorbitol as the gelator.

PubMed

Lan, Yaqi; Corradini, Maria G; Liu, Xia; May, Tim E; Borondics, Ferenc; Weiss, Richard G; Rogers, Michael A

2014-12-02

Solvent properties play a central role in mediating the aggregation and self-assembly of molecular gelators and their growth into fibers. Numerous attempts have been made to correlate the solubility parameters of solvents and gelation abilities of molecular gelators, but a comprehensive comparison of the most important parameters has yet to appear. Here, the degree to which partition coefficients (log P), Henry's law constants (HLC), dipole moments, static relative permittivities (ε(r)), solvatochromic E(T)(30) parameters, Kamlet-Taft parameters (β, α, and π), Catalan's solvatochromic parameters (SPP, SB, and SA), Hildebrand solubility parameters (δ(i)), and Hansen solubility parameters (δ(p), δ(d), δ(h)) and the associated Hansen distance (R(ij)) of 62 solvents (covering a wide range of properties) can be correlated with the self-assembly and gelation of 1,3:2,4-dibenzylidene sorbitol (DBS) gelation, a classic molecular gelator, is assessed systematically. The approach presented describes the basis for each of the parameters and how it can be applied. As such, it is an instructional blueprint for how to assess the appropriate type of solvent parameter for use with other molecular gelators as well as with molecules forming other types of self-assembled materials. The results also reveal several important insights into the factors favoring the gelation of solvents by DBS. The ability of a solvent to accept or donate a hydrogen bond is much more important than solvent polarity in determining whether mixtures with DBS become solutions, clear gels, or opaque gels. Thermodynamically derived parameters could not be correlated to the physical properties of the molecular gels unless they were dissected into their individual HSPs. The DBS solvent phases tend to cluster in regions of Hansen space and are highly influenced by the hydrogen-bonding HSP, δ(h). It is also found that the fate of this molecular gelator, unlike that of polymers, is influenced not only by the magnitude of the distance between the HSPs for DBS and the HSPs of the solvent, R(ij), but also by the directionality of R(ij): if the solvent has a larger hydrogen-bonding HSP (indicating stronger H-bonding) than that of the DBS, then clear gels are formed; opaque gels form when the solvent has a lower δ(h) than does DBS.

Induced liquid-crystalline ordering in solutions of stiff and flexible amphiphilic macromolecules: Effect of mixture composition

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

Glagolev, Mikhail K.; Vasilevskaya, Valentina V., E-mail: vvvas@polly.phys.msu.ru; Khokhlov, Alexei R.

Impact of mixture composition on self-organization in concentrated solutions of stiff helical and flexible macromolecules was studied by means of molecular dynamics simulation. The macromolecules were composed of identical amphiphilic monomer units but a fraction f of macromolecules had stiff helical backbones and the remaining chains were flexible. In poor solvents the compacted flexible macromolecules coexist with bundles or filament clusters from few intertwined stiff helical macromolecules. The increase of relative content f of helical macromolecules leads to increase of the length of helical clusters, to alignment of clusters with each other, and then to liquid-crystalline-like ordering along a singlemore » direction. The formation of filament clusters causes segregation of helical and flexible macromolecules and the alignment of the filaments induces effective liquid-like ordering of flexible macromolecules. A visual analysis and calculation of order parameter relaying the anisotropy of diffraction allow concluding that transition from disordered to liquid-crystalline state proceeds sharply at relatively low content of stiff components.« less

Adsorbed molecules in external fields: Effect of confining potential.

PubMed

Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

2016-12-05

We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular dynamics simulation of the structure and dynamics of 5-HT3 serotonin receptor

NASA Astrophysics Data System (ADS)

Antonov, M. Yu.; Popinako, A. V.; Prokopiev, G. A.

2016-10-01

In this work, we investigated structure, dynamics and ion transportation in transmembrane domain of the 5-HT3 serotonin receptor. High-resolution (0.35 nm) structure of the 5-HT3 receptor in complex with stabilizing nanobodies was determined by protein crystallography in 2014 (Protein data bank (PDB) code 4PIR). Transmembrane domain of the structure was prepared in complex with explicit membrane environment (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)) and solvent (TIP3P water model). Molecular dynamics protocols for simulation and stabilization of the transmembrane domain of the 5-HT3 receptor model were developed and 60 ns simulation of the structure was conducted in order to explore structural parameters of the system. We estimated the mean force profile for Na+ ions using umbrella sampling method.

3D molecular models of whole HIV-1 virions generated with cellPACK

PubMed Central

Goodsell, David S.; Autin, Ludovic; Forli, Stefano; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology. PMID:25253262

Structure and dynamics of complex liquid water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

S, Indrajith V.; Natesan, Baskaran

2015-06-01

We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

The nu sub 2 band CHD3; ground state parameters for CHD3 from combination differences

NASA Technical Reports Server (NTRS)

Jennings, D. E.; Blass, W. E.

1974-01-01

The nu sub 2 fundamental band of CHD3, centered near 2143/cm, was recorded at a resolution of 0.015-0.25/cm. Analysis of ground state combination differences yielded well-determined values for the ground state molecular parameters for CHD3. These parameters were used in the determination of the alpha and beta molecular parameters for nu sub 2.

Delivery of Cisplatin Anti-Cancer Drug from Carbon, Boron Nitride, and Silicon Carbide Nanotubes Forced by Ag-Nanowire: A Comprehensive Molecular Dynamics Study.

PubMed

Mehrjouei, Esmat; Akbarzadeh, Hamed; Shamkhali, Amir Nasser; Abbaspour, Mohsen; Salemi, Sirous; Abdi, Pooya

2017-07-03

In this work, liberation of cisplatin molecules from interior of a nanotube due to entrance of an Ag-nanowire inside it was simulated by classical molecular dynamics method. The aim of this simulation was investigation on the effects of diameter, chirality, and composition of the nanotube, as well as the influence of temperature on this process. For this purpose, single walled carbon, boron nitride, and silicon carbide nanotube were considered. In order for a more concise comparison of the results, a new parameter namely efficiency of drug release, was introduced. The results demonstrated that the efficiency of drug release is sensitive to its adsorption on outer surface of the nanotube. Moreover, this efficiency is also sensitive to the nanotube composition and its diameter. For the effect of nanotube composition, the results indicated that silicon carbide nanotube has the least efficiency for drug release, due to its strong drug-nanotube. Also, the most important acting forces on drug delivery are van der Waals interactions. Finally, the kinetic of drug release is fast and is not related to the structural parameters of the nanotube and temperature, significantly.

Nano and microparticle engineering of water insoluble drugs using a novel spray-drying process.

PubMed

Schafroth, Nina; Arpagaus, Cordin; Jadhav, Umesh Y; Makne, Sushil; Douroumis, Dennis

2012-02-01

In the current study nano and microparticle engineering of water insoluble drugs was conducted using a novel piezoelectric spray-drying approach. Cyclosporin A (CyA) and dexamethasone (DEX) were encapsulated in biodegradable poly(D,L-lactide-co-glycolide) (PLGA) grades of different molecular weights. Spray-drying studies carried out with the Nano Spray Dryer B-90 employed with piezoelectric driven actuator. The processing parameters including inlet temperature, spray mesh diameter, sample flow rate, spray rate, applied pressure and sample concentration were examined in order to optimize the particle size and the obtained yield. The process parameters and the solute concentration showed a profound effect on the particle engineering and the obtained product yield. The produced powder presented consistent and reproducible spherical particles with narrow particle size distribution. Cyclosporin was found to be molecularly dispersed while dexamethasone was in crystalline state within the PLGA nanoparticles. Further evaluation revealed excellent drug loading, encapsulation efficiency and production yield. In vitro studies demonstrated sustained release patterns for the active substances. This novel spray-drying process proved to be efficient for nano and microparticle engineering of water insoluble active substances. Copyright © 2011 Elsevier B.V. All rights reserved.

Spatial fluorescence cross-correlation spectroscopy between core and ring pinholes

NASA Astrophysics Data System (ADS)

Blancquaert, Yoann; Delon, Antoine; Derouard, Jacques; Jaffiol, Rodolphe

2006-04-01

Fluorescence Correlation Spectroscopy (FCS) is an attractive method to measure molecular concentration, mobility parameters and chemical kinetics. However its ability to descriminate different diffusing species needs to be improved. Recently, we have proposed a simplified spatial Fluorescence cross Correlation Spectroscopy (sFCCS) method, allowing, with only one focused laser beam to obtain two confocal volumes spatially shifted. Now, we present a new sFCCS optical geometry where the two pinholes, a ring and core, are encapsulated one in the other. In this approach all physical and chemical processes that occur in a single volume, like singlet-triplet dynamics and photobleaching, can be eliminated; moreover, this new optical geometry optimises the collection of fluorescence. The first cross Correlation curves for Rhodamine 6G (Rh6G) in Ethanol are presented, in addition to the effect of the size of fluorescent particules (nano-beads, diameters : 20, 100 and 200 nm). The relative simplicity of the method leads us to propose sFCCS as an appropriate method for the determination of diffusion parameters of fluorophores in solution or cells. Nevertheless, progresses in the ingeniering of the optical Molecular Detection Efficiency volumes are highly desirable, in order to improve the descrimination between the cross correlated volumes.

Quantitative structure activity relationship studies of piperazinyl phenylalanine derivatives as VLA-4/VCAM-1 inhibitors.

PubMed

Bhargava, Dinesh; Karthikeyan, C; Moorthy, N S H N; Trivedi, Piyush

2009-09-01

QSAR study was carried out for a series of piperazinyl phenylalanine derivatives exhibiting VLA-4/VCAM-1 inhibitory activity to find out the structural features responsible for the biological activity. The QSAR study was carried out on V-life Molecular Design Suite software and the derived best QSAR model by partial least square (forward) regression method showed 85.67% variation in biological activity. The statistically significant model with high correlation coefficient (r2=0.85) was selected for further study and the resulted validation parameters of the model, crossed squared correlation coefficient (q2=0.76 and pred_r2=0.42) show the model has good predictive ability. The model showed that the parameters SaaNEindex, SsClcount slogP,and 4PathCount are highly correlated with VLA-4/VCAM-1 inhibitory activity of piperazinyl phenylalanine derivatives. The result of the study suggests that the chlorine atoms in the molecule and fourth order fragmentation patterns in the molecular skeleton favour VLA-4/VCAM-1 inhibition shown by the title compounds whereas lipophilicity and nitrogen bonded to aromatic bond are not conducive for VLA-4/VCAM-1 inhibitory activity.

X-ray detectability of accreting isolated black holes in our Galaxy

NASA Astrophysics Data System (ADS)

Tsuna, Daichi; Kawanaka, Norita; Totani, Tomonori

2018-06-01

Detectability of isolated black holes (IBHs) without a companion star but emitting X-rays by accretion from dense interstellar medium (ISM) or molecular cloud gas is investigated. We calculate orbits of IBHs in the Galaxy to derive a realistic spatial distribution of IBHs for various mean values of kick velocity at their birth υavg. X-ray luminosities of these IBHs are then calculated considering various phases of ISM and molecular clouds for a wide range of the accretion efficiency λ (a ratio of the actual accretion rate to the Bondi rate) that is rather uncertain. It is found that detectable IBHs mostly reside near the Galactic Centre (GC), and hence taking the Galactic structure into account is essential. In the hard X-ray band, where identification of IBHs from other contaminating X-ray sources may be easier, the expected number of IBHs detectable by the past survey by NuSTAR towards GC is at most order unity. However, 30-100 IBHs may be detected by the future survey by FORCE with an optimistic parameter set of υavg = 50 km s-1 and λ = 0.1, implying that it may be possible to detect IBHs or constrain the model parameters.

Algorithms and physical parameters involved in the calculation of model stellar atmospheres

NASA Astrophysics Data System (ADS)

Merlo, D. C.

This contribution summarizes the Doctoral Thesis presented at Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba for the degree of PhD in Astronomy. We analyze some algorithms and physical parameters involved in the calculation of model stellar atmospheres, such as atomic partition functions, functional relations connecting gaseous and electronic pressure, molecular formation, temperature distribution, chemical compositions, Gaunt factors, atomic cross-sections and scattering sources, as well as computational codes for calculating models. Special attention is paid to the integration of hydrostatic equation. We compare our results with those obtained by other authors, finding reasonable agreement. We make efforts on the implementation of methods that modify the originally adopted temperature distribution in the atmosphere, in order to obtain constant energy flux throughout. We find limitations and we correct numerical instabilities. We integrate the transfer equation solving directly the integral equation involving the source function. As a by-product, we calculate updated atomic partition functions of the light elements. Also, we discuss and enumerate carefully selected formulae for the monochromatic absorption and dispersion of some atomic and molecular species. Finally, we obtain a flexible code to calculate model stellar atmospheres.

Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST.

PubMed

Baele, Guy; Lemey, Philippe; Rambaut, Andrew; Suchard, Marc A

2017-06-15

Advances in sequencing technology continue to deliver increasingly large molecular sequence datasets that are often heavily partitioned in order to accurately model the underlying evolutionary processes. In phylogenetic analyses, partitioning strategies involve estimating conditionally independent models of molecular evolution for different genes and different positions within those genes, requiring a large number of evolutionary parameters that have to be estimated, leading to an increased computational burden for such analyses. The past two decades have also seen the rise of multi-core processors, both in the central processing unit (CPU) and Graphics processing unit processor markets, enabling massively parallel computations that are not yet fully exploited by many software packages for multipartite analyses. We here propose a Markov chain Monte Carlo (MCMC) approach using an adaptive multivariate transition kernel to estimate in parallel a large number of parameters, split across partitioned data, by exploiting multi-core processing. Across several real-world examples, we demonstrate that our approach enables the estimation of these multipartite parameters more efficiently than standard approaches that typically use a mixture of univariate transition kernels. In one case, when estimating the relative rate parameter of the non-coding partition in a heterochronous dataset, MCMC integration efficiency improves by > 14-fold. Our implementation is part of the BEAST code base, a widely used open source software package to perform Bayesian phylogenetic inference. guy.baele@kuleuven.be. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Molecular line emission models of Herbig-Haro objects. II - HCO(+) emission

NASA Technical Reports Server (NTRS)

Wolfire, Mark G.; Koenigl, Arieh

1993-01-01

We present time-dependent models of the chemistry and temperature of interstellar molecular gas clumps that are exposed to the radiation from propagating stellar-jet shocks. The X-ray, EUV, and FUV radiation from the shock initiates ion chemistry and also heats the gas in the clumps. Using representative parameters, we show that, on the shock transit time between the clumps, the abundances of the ionized molecular species that are produced in the clumps can exceed the values determined from steady state models by several orders of magnitude. Collisional excitation by the heated gas can lead to measurable line emission from several ionized species; as in previous investigations of X-ray-irradiated molecular gas, we find that electron impacts contribute significantly to this process. We apply these results to the interpretation of the HCO(+) line emission that has already been detected in several Herbig-Haro objects. We demonstrate that this picture provides a natural explanation of the fact that the line intensity typically peaks ahead of the associated shock, as well as of the reported low line-center velocities and narrow line widths. We tabulate several diagnostic line intensities of HCO(+) and other molecular species that may be used to infer the physical conditions in the emitting gas.

Mechanical integrity of a carbon nanotube/copper-based through-silicon via for 3D integrated circuits: a multi-scale modeling approach.

PubMed

Awad, Ibrahim; Ladani, Leila

2015-12-04

Carbon nanotube (CNT)/copper (Cu) composite material is proposed to replace Cu-based through-silicon vias (TSVs) in micro-electronic packages. The proposed material is believed to offer extraordinary mechanical and electrical properties and the presence of CNTs in Cu is believed to overcome issues associated with miniaturization of Cu interconnects, such as electromigration. This study introduces a multi-scale modeling of the proposed TSV in order to evaluate its mechanical integrity under mechanical and thermo-mechanical loading conditions. Molecular dynamics (MD) simulation was used to determine CNT/Cu interface adhesion properties. A cohesive zone model (CZM) was found to be most appropriate to model the interface adhesion, and CZM parameters at the nanoscale were determined using MD simulation. CZM parameters were then used in the finite element analysis in order to understand the mechanical and thermo-mechanical behavior of composite TSV at micro-scale. From the results, CNT/Cu separation does not take place prior to plastic deformation of Cu in bending, and separation does not take place when standard thermal cycling is applied. Further investigation is recommended in order to alleviate the increased plastic deformation in Cu at the CNT/Cu interface in both loading conditions.

A group contribution method for associating chain molecules based on the statistical associating fluid theory (SAFT-γ)

NASA Astrophysics Data System (ADS)

Lymperiadis, Alexandros; Adjiman, Claire S.; Galindo, Amparo; Jackson, George

2007-12-01

A predictive group-contribution statistical associating fluid theory (SAFT-γ) is developed by extending the molecular-based SAFT-VR equation of state [A. Gil-Villegas et al. J. Chem. Phys. 106, 4168 (1997)] to treat heteronuclear molecules which are formed from fused segments of different types. Our models are thus a heteronuclear generalization of the standard models used within SAFT, comparable to the optimized potentials for the liquid state OPLS models commonly used in molecular simulation; an advantage of our SAFT-γ over simulation is that an algebraic description for the thermodynamic properties of the model molecules can be developed. In our SAFT-γ approach, each functional group in the molecule is modeled as a united-atom spherical (square-well) segment. The different groups are thus characterized by size (diameter), energy (well depth) and range parameters representing the dispersive interaction, and by shape factor parameters (which denote the extent to which each group contributes to the overall molecular properties). For associating groups a number of bonding sites are included on the segment: in this case the site types, the number of sites of each type, and the appropriate association energy and range parameters also have to be specified. A number of chemical families (n-alkanes, branched alkanes, n-alkylbenzenes, mono- and diunsaturated hydrocarbons, and n-alkan-1-ols) are treated in order to assess the quality of the SAFT-γ description of the vapor-liquid equilibria and to estimate the parameters of various functional groups. The group parameters for the functional groups present in these compounds (CH3, CH2, CH3CH, ACH, ACCH2, CH2, CH , and OH) together with the unlike energy parameters between groups of different types are obtained from an optimal description of the pure component phase equilibria. The approach is found to describe accurately the vapor-liquid equilibria with an overall %AAD of 3.60% for the vapor pressure and 0.86% for the saturated liquid density. The fluid phase equilibria of some larger compounds comprising these groups, which are not included in the optimization database and some binary mixtures are examined to confirm the predictive capability of the SAFT-γ approach. A key advantage of our method is that the binary interaction parameters between groups can be estimated directly from an examination of pure components alone. This means that as a first approximation the fluid-phase equilibria of mixtures of compounds comprising the groups considered can be predicted without the need for any adjustment of the binary interaction parameters (which is common in other approaches). The special case of molecular models comprising tangentially bonded (all-atom and united-atom) segments is considered separately; we comment on the adequacy of such models in representing the properties of real molecules.

A group contribution method for associating chain molecules based on the statistical associating fluid theory (SAFT-gamma).

PubMed

Lymperiadis, Alexandros; Adjiman, Claire S; Galindo, Amparo; Jackson, George

2007-12-21

A predictive group-contribution statistical associating fluid theory (SAFT-gamma) is developed by extending the molecular-based SAFT-VR equation of state [A. Gil-Villegas et al. J. Chem. Phys. 106, 4168 (1997)] to treat heteronuclear molecules which are formed from fused segments of different types. Our models are thus a heteronuclear generalization of the standard models used within SAFT, comparable to the optimized potentials for the liquid state OPLS models commonly used in molecular simulation; an advantage of our SAFT-gamma over simulation is that an algebraic description for the thermodynamic properties of the model molecules can be developed. In our SAFT-gamma approach, each functional group in the molecule is modeled as a united-atom spherical (square-well) segment. The different groups are thus characterized by size (diameter), energy (well depth) and range parameters representing the dispersive interaction, and by shape factor parameters (which denote the extent to which each group contributes to the overall molecular properties). For associating groups a number of bonding sites are included on the segment: in this case the site types, the number of sites of each type, and the appropriate association energy and range parameters also have to be specified. A number of chemical families (n-alkanes, branched alkanes, n-alkylbenzenes, mono- and diunsaturated hydrocarbons, and n-alkan-1-ols) are treated in order to assess the quality of the SAFT-gamma description of the vapor-liquid equilibria and to estimate the parameters of various functional groups. The group parameters for the functional groups present in these compounds (CH(3), CH(2), CH(3)CH, ACH, ACCH(2), CH(2)=, CH=, and OH) together with the unlike energy parameters between groups of different types are obtained from an optimal description of the pure component phase equilibria. The approach is found to describe accurately the vapor-liquid equilibria with an overall %AAD of 3.60% for the vapor pressure and 0.86% for the saturated liquid density. The fluid phase equilibria of some larger compounds comprising these groups, which are not included in the optimization database and some binary mixtures are examined to confirm the predictive capability of the SAFT-gamma approach. A key advantage of our method is that the binary interaction parameters between groups can be estimated directly from an examination of pure components alone. This means that as a first approximation the fluid-phase equilibria of mixtures of compounds comprising the groups considered can be predicted without the need for any adjustment of the binary interaction parameters (which is common in other approaches). The special case of molecular models comprising tangentially bonded (all-atom and united-atom) segments is considered separately; we comment on the adequacy of such models in representing the properties of real molecules.

COLLABORATIVE RESEARCH AND DEVELOPMENT (CR&D) Delivery Order 0059: Molecular Dynamics Modeling Support

DTIC Science & Technology

2008-03-01

Molecular Dynamics Simulations 5 Theory: Equilibrium Molecular Dynamics Simulations 6 Theory: Non...Equilibrium Molecular Dynamics Simulations 8 Carbon Nanotube Simulations : Approach and results from equilibrium and non-equilibrium molecular dynamics ...touched from the perspective of molecular dynamics simulations . However, ordered systems such as “Carbon Nanotubes” have been investigated in terms

Molecular Design for Preparation of Hexagonal-Ordered Porous Films Based on Side-chain Type Liquid-Crystalline Star Polymer.

PubMed

Naka, Yumiko; Takayama, Hiromu; Koyama, Teruhisa; Le, Khoa V; Sasaki, Takeo

2018-05-02

Fabrication of regularly porous films by the breath-figure method has attracted much attention. The simple, low-cost technique uses the condensation of water droplets to produce these structures, but the phenomenon itself is complex, requiring control over many interacting parameters that change throughout the process. Developing a unified understanding for the molecular design of polymers to prepare ordered porous films is challenging, but required for further advancements. In this article, the effects of the chemical structure of polymers in the breath-figure technique were systematically explored using side-chain type liquid-crystalline (LC) star polymers. The formation of porous films was affected by the structure of the polymers. Although the entire film surface of poly(11-[4-(4-cyanobiphenyl)oxy]undecyl methacrylate) (P11CB) had a hexagonal ordered porous structure over a certain Mn value, regularly arranged holes did not easily form in poly(methyl methacrylate) (PMMA), even though the main chain of PMMA is similar to that of P11CB. Comparing P11CB and poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11B) (P11CB without cyano groups) showed that the local polar groups in hydrophobic polymers promoted the formation of ordered porous films. No holes formed in poly(4-cyanobiphenyl methacrylate) (P0CB) (P11CB without alkyl spacers) films due to its hydrophilicity. The introduction of alkyl chains in P0CB allowed the preparation of honeycomb-structured films by increasing the internal tension. However, alkyl chains in the side chain alone did not result in a porous structure, as in the case of poly(11-[(1,1'-biphenyl)-4-yloxy]undecyl methacrylate) (P11). Aromatic rings are also required to increase the Tg and improve film formability. In the present study, suitable molecular designs of polymers were found, specifically hydrophobic polymers with local polar groups, to form a regularly porous structure. Development of clear guidelines for the molecular design of polymers is the subject of our current research, which will enable the fabrication of porous films using various functional polymers.

Effects of different self-assembled monolayers on thin-film morphology: a combined DFT/MD simulation protocol.

PubMed

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Motta, Alessandro; Nicolotti, Orazio; Lattanzi, Gianluca

2015-10-06

Organic thin film transistors (OTFTs) are multilayer field-effect transistors that employ an organic conjugated material as semiconductor. Several experimental groups have recently demonstrated that the insertion of an organic self-assembled monolayer (SAM) between the dielectric and the semiconductive layer is responsible for a sensible improvement of the OTFT performances in terms of an increased charge carrier mobility caused by a higher degree of order in the organic semiconductor layer. Here, we describe a combined periodic density functional theory (DFT) and classical molecular dynamics (MD) protocol applied to four different SAMs and a pentacene monolayer deposited onto their surfaces. In particular, we investigate the morphology and the surface of the four SAMs and the translational, orientational, and nematic order of the monolayer through the calculation of several distribution functions and order parameters pointing out the differences among the systems and relating them to known experimental results. Our calculations also suggest that small differences in the SAM molecular design will produce remarkable differences in the SAM surface and monolayer order. In particular, our simulations explain how a SAM with a bulky terminal group results in an irregular and rough surface that determines the deposition of a disordered semiconductive monolayer. On the contrary, SAMs with a small terminal group generate smooth surfaces with uninterrupted periodicity, thus favoring the formation of an ordered pentacene monolayer that increases the mobility of charge carriers and improves the overall performances of the OTFT devices. Our results clearly point out that the in silico procedure presented here might be of help in tuning the design of SAMs in order to improve the quality of OTFT devices.

Density functional theory molecular modeling and antimicrobial behaviour of selected 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Cinteza, Ludmila Otilia; Marton, George Iuliu; Marutescu, Luminita Gabriela; Chifiriuc, Mariana-Carmen; Constantinescu, Catalin

2017-09-01

A series of 9-substituted 1,2,3,4,5,6,7,8-octahydroacridine-N(10)-oxides is evaluated against 12 bacterial and fungal strains, for their microbicidal and anti-pathogenic features. The largest spectrum of the antibacterial activity is evidenced for the nitro- (2b) and hydroxy- (5b) N-oxides, followed by the amino-N-oxide (3b). Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied/lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software at M11/ktzvp level of theory in order to find their structural and electronic parameters. We show that the planarity of the molecules and the presence of the electron withdrawing group are advantages for its antimicrobial activity. Finally, we briefly present and discuss results on the processing of such compounds into thin films and hybrid structures by laser-assisted techniques, i.e. matrix-assisted pulsed laser evaporation (MAPLE) or laser-induced forward transfer (LIFT), to provide simple and environmental friendly, state-of-the-art solutions for antimicrobial/medical coatings and devices.

The Optical Bichromatic Force in Molecular Systems

NASA Astrophysics Data System (ADS)

Aldridge, Leland; Galica, Scott; Eyler, E. E.

2015-05-01

The optical bichromatic force has been demonstrated to be useful for slowing atomic beams much more rapidly than radiative forces. Through numerical simulations, we examine several aspects of applying the bichromatic force to molecular beams. One is the unavoidable existence of out-of-system radiative decay, requiring one or more repumping beams. We find that the average deceleration varies strongly with the repumping intensity, but when using optimal parameters, the force approaches the limiting value allowed by population statistics. Another consideration is the effect of fine and hyperfine structure. We examine a simplified multlevel model based on the B <--> X transition in calcium monofluoride. To circumvent optical pumping into coherent dark states, we include two possible schemes: (1) a skewed dc magnetic field, and (2) rapid optical polarization switching. Our results indicate that the bichromatic force remains a viable option for creating large forces in molecular beams, with a reduction in the peak force by approximately an order of magnitude compared to a two-level atom, but little effect on the velocity range over which the force is effective. We also describe our progress towards experimental tests of the bichromatic force on a molecular beam of CaF. Supported by the National Science Foundation.

Molecular design for nonpolar chiral-axial quadratic nonlinear optics

NASA Astrophysics Data System (ADS)

Wiggers, Gregory A.

In this thesis the hyperpolarizability of various multi-dimensional molecules is studied theoretically/computationally, with particular focus on the second-rank Kleinman-disallowed (KD) component of the hyperpolarizability. This component, which transforms as a second-rank traceless symmetric tensor, could be utilized in certain chiral-axial molecular alignment schemes to produce a bulk response. Nonpolar chiral-axial systems have been proposed in contrast to polar media, which utilize the vector component of the molecular hyperpolarizability and require parallel alignment of the molecular dipoles. Such parallel alignment of dipoles must be "frozen in" in order to overcome the natural tendency for dipoles to align anti-parallel. This limits the density of chromophores that can be loaded into a polar material. Nonpolar materials do not have such limits in theory. The two geometric classes of molecules that can most easily be incorporated into nonpolar chiral-uniaxial materials are propeller-shaped (C3 or D3 symmetry) and Λ-shaped (C2v symmetry). This work describes efforts to design molecules within these classes that would be suitable for bulk NLO materials. The sum-over-states (SOS) expression is used to model the molecular hyperpolarizability, and quantum chemical calculations, along with linear absorption data (when available) provide the necessary parameters to evaluate truncated forms of the SOS expression. A host of chemical and geometric modifications will be considered in order to elucidate important structure/function relationships. Also, the SOS model will be tested in some cases when experimental measurements (via Kleinman-disallowed hyper-Rayleigh scattering) are available. While a majority of this work focuses on multi-dimensional molecules, a small section deals with the question of optimizing the hyperpolarizability of a one-dimensional system. It is suggested that the recently-proposed idea of "modulated conjugation" as a means for improving intrinsic molecular hyperpolarizability is based on subtle misinterpretations of computational results. Even so, the concept of modulated conjugation may lead to improved hyperpolarizabilities and possible reasons are discussed.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

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

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

Modeling charge transport in organic photovoltaic materials.

PubMed

Nelson, Jenny; Kwiatkowski, Joe J; Kirkpatrick, James; Frost, Jarvist M

2009-11-17

The performance of an organic photovoltaic cell depends critically on the mobility of charge carriers within the constituent molecular semiconductor materials. However, a complex combination of phenomena that span a range of length and time scales control charge transport in disordered organic semiconductors. As a result, it is difficult to rationalize charge transport properties in terms of material parameters. Until now, efforts to improve charge mobilities in molecular semiconductors have proceeded largely by trial and error rather than through systematic design. However, recent developments have enabled the first predictive simulation studies of charge transport in disordered organic semiconductors. This Account describes a set of computational methods, specifically molecular modeling methods, to simulate molecular packing, quantum chemical calculations of charge transfer rates, and Monte Carlo simulations of charge transport. Using case studies, we show how this combination of methods can reproduce experimental mobilities with few or no fitting parameters. Although currently applied to material systems of high symmetry or well-defined structure, further developments of this approach could address more complex systems such anisotropic or multicomponent solids and conjugated polymers. Even with an approximate treatment of packing disorder, these computational methods simulate experimental mobilities within an order of magnitude at high electric fields. We can both reproduce the relative values of electron and hole mobility in a conjugated small molecule and rationalize those values based on the symmetry of frontier orbitals. Using fully atomistic molecular dynamics simulations of molecular packing, we can quantitatively replicate vertical charge transport along stacks of discotic liquid crystals which vary only in the structure of their side chains. We can reproduce the trends in mobility with molecular weight for self-organizing polymers using a cheap, coarse-grained structural simulation method. Finally, we quantitatively reproduce the field-effect mobility in disordered C60 films. On the basis of these results, we conclude that all of the necessary building blocks are in place for the predictive simulation of charge transport in macromolecular electronic materials and that such methods can be used as a tool toward the future rational design of functional organic electronic materials.

Vibrational spectroscopy investigation and density functional theory calculations on (E)-N‧-(4-methoxybenzylidene) benzohydrazide

NASA Astrophysics Data System (ADS)

Saleem, H.; Subashchandrabose, S.; Ramesh Babu, N.; Syed Ali Padusha, M.

2015-05-01

The FT-IR, FT-Raman and UV-Vis spectra of the Schiff base compound (E)-N‧-(4-methoxybenzylidene) benzohydrazide (MBBH) have been recorded and analyzed. The optimized geometrical parameters were calculated. The complete vibrational assignments were performed on the basis of TED of the vibrational modes, calculated with the help of SQM method. NBO analysis has been carried out to explore the hyperconjugative interactions and their second order stabilization energy within the molecule. The molecular orbitals (MO's) and its energy gap were studied. The first order hyperpolarizability (β0) and related properties (β, α0, Δα) of MBBH are also calculated. All theoretical calculations were performed on the basis of B3LYP/6-311++G(d,p) level of theory.

A predictive model for failure properties of thermoset resins

NASA Technical Reports Server (NTRS)

Caruthers, James M.; Bowles, Kenneth J.

1989-01-01

A predictive model for the three-dimensional failure behavior of engineering polymers has been developed in a recent NASA-sponsored research program. This model acknowledges the underlying molecular deformation mechanisms and thus accounts for the effects of different chemical compositions, crosslink density, functionality of the curing agent, etc., on the complete nonlinear stress-strain response including yield. The material parameters required by the model can be determined from test-tube quantities of a new resin in only a few days. Thus, we can obtain a first-order prediction of the applicability of a new resin for an advanced aerospace application without synthesizing the large quantities of material needed for failure testing. This technology will effect order-of-magnitude reductions in the time and expense required to develop new engineering polymers.

Analyses of kinetic glass transition in short-range attractive colloids based on time-convolutionless mode-coupling theory.

PubMed

Narumi, Takayuki; Tokuyama, Michio

2017-03-01

For short-range attractive colloids, the phase diagram of the kinetic glass transition is studied by time-convolutionless mode-coupling theory (TMCT). Using numerical calculations, TMCT is shown to recover all the remarkable features predicted by the mode-coupling theory for attractive colloids: the glass-liquid-glass reentrant, the glass-glass transition, and the higher-order singularities. It is also demonstrated through the comparisons with the results of molecular dynamics for the binary attractive colloids that TMCT improves the critical values of the volume fraction. In addition, a schematic model of three control parameters is investigated analytically. It is thus confirmed that TMCT can describe the glass-glass transition and higher-order singularities even in such a schematic model.

Development of solid-state NMR techniques for the characterisation of pharmaceutical compounds

NASA Astrophysics Data System (ADS)

Tatton, Andrew S.

Structural characterisation in the solid state is an important step in understanding the physical and chemical properties of a material. Solid-state NMR techniques applied to solid delivery forms are presented as an alternative to more established structural characterisation methods. The effect of homonuclear decoupling upon heteronuclear couplings is investigated using a combination of experimental and density-matrix simulation results acquired from a 13C-1H spinecho pulse sequence, modulated by scalar couplings. It is found that third-order cross terms under MAS and homonuclear decoupling contribute to strong dephasing effects in the NMR signal. Density-matrix simulations allow access to parameters currently unattainable in experiment, and demonstrate that higher homonuclear decoupling rf nutation frequencies reduce the magnitude of third-order cross terms. 15N-1H spinecho experiments were applied to pharmaceutically relevant samples to differentiate between the number of directly attached protons. Using this method, proton transfer in an acid-base reaction is proven in pharmaceutical salts. The indirect detection of 14N lineshapes via protons obtained using 2D 14N-1H HMQC experiments is presented, where coherence transfer is achieved via heteronuclear through-space dipolar couplings. The importance of fast MAS frequencies is demonstrated, and it is found that increasing the recoupling duration reveals longer range NH proximities. The 2D 14N-1H HMQC method is used to demonstrate the presence of specific hydrogen bonding interactions, and thus aid in identifying molecular association in a cocrystal and an amorphous dispersion. In addition, hydrogen bonding motifs were identified by observing the changes in the 14N quadrupolar parameters between individual molecular components relative to the respective solid delivery form. First-principles calculations of NMR chemical shifts and quadrupolar parameters using the GIPAW method were combined with 14N-1H experimental results to assist with spectral assignment and the identification of the hydrogen bonding interactions.

Developmant of a Reparametrized Semi-Empirical Force Field to Compute the Rovibrational Structure of Large PAHs

NASA Astrophysics Data System (ADS)

Fortenberry, Ryan

The Spitzer Space Telescope observation of spectra most likely attributable to diverse and abundant populations of polycyclic aromatic hydrocarbons (PAHs) in space has led to tremendous interest in these molecules as tracers of the physical conditions in different astrophysical regions. A major challenge in using PAHs as molecular tracers is the complexity of the spectral features in the 3-20 μm region. The large number and vibrational similarity of the putative PAHs responsible for these spectra necessitate determination for the most accurate basis spectra possible for comparison. It is essential that these spectra be established in order for the regions explored with the newest generation of observatories such as SOFIA and JWST to be understood. Current strategies to develop these spectra for individual PAHs involve either matrixisolation IR measurements or quantum chemical calculations of harmonic vibrational frequencies. These strategies have been employed to develop the successful PAH IR spectral database as a repository of basis functions used to fit astronomically observed spectra, but they are limited in important ways. Both techniques provide an adequate description of the molecules in their electronic, vibrational, and rotational ground state, but these conditions do not represent energetically hot regions for PAHs near strong radiation fields of stars and are not direct representations of the gas phase. Some non-negligible matrix effects are known in condensed-phase studies, and the inclusion of anharmonicity in quantum chemical calculations is essential to generate physically-relevant results especially for hot bands. While scaling factors in either case can be useful, they are agnostic to the system studied and are not robustly predictive. One strategy that has emerged to calculate the molecular vibrational structure uses vibrational perturbation theory along with a quartic force field (QFF) to account for higher-order derivatives of the potential energy surface. QFFs can regularly predict the fundamental vibrational frequencies to within 5 cm-1 of experimentally measured values. This level of accuracy represents a reduction in discrepancies by an order of magnitude compared with harmonic frequencies calculated with density functional theory (DFT). The major limitation of the QFF strategy is that the level of electronic-structure theory required to develop a predictive force field is prohibitively time consuming for molecular systems larger than 5 atoms. Recent advances in QFF techniques utilizing informed DFT approaches have pushed the size of the systems studied up to 24 heavy atoms, but relevant PAHs can have up to hundreds of atoms. We have developed alternative electronic-structure methods that maintain the accuracy of the coupled-cluster calculations extrapolated to the complete basis set limit with relativistic and core correlation corrections applied: the CcCR QFF. These alternative methods are based on simplifications of Hartree—Fock theory in which the computationally intensive two-electron integrals are approximated using empirical parameters. These methods reduce computational time to orders of magnitude less than the CcCR calculations. We have derived a set of optimized empirical parameters to minimize the difference molecular ions of astrochemical significance. We have shown that it is possible to derive a set of empirical parameters that will produce RMS energy differences of less than 2 cm- 1 for our test systems. We are proposing to adopt this reparameterization strategy and some of the lessons learned from the informed DFT studies to create a semi-empirical method whose tremendous speed will allow us to study the rovibrational structure of large PAHs with up to 100s of carbon atoms.

The interaction of sodium dodecyl sulfate and urea with cat-fish collagen solutions in acetate buffer: hydrodynamic and thermodynamic studies.

PubMed

Rose, C; Mandal, A B

1996-02-01

Cat-fish collagen was extracted and characterized. Shrinkage temperature of cat-fish collagen is 54.5 degrees C. SDS-PAGE pattern indicated that the cat-fish collagen is Type I in nature. The ratio of proline and hydroxyproline is 1:2 and it suggests cat-fish collagen is vertebrate. The molecular weight of cat-fish collagen was determined by using molecular sieve chromatography and it was found to be 3 20,000 Da. The mutual interaction of cat-fish collagen with SDS and urea was studied at various temperatures. The results suggest that the aggregation of collagen is facilitated by the presence of SDS, whereas hindered by urea. The various thermodynamic parameters were estimated from viscosity measurements and the transfer of collagen into SDS micelles, urea and the reverse phenomenon was analysed. These transfer properties are temperature-dependent. Our thermodynamic results are also able to predict the exact denaturation temperature as well as the structural order of water in the collagen in various environments. The hydrated volumes, Vh of collagen in buffer, SDS, and urea environments using Simha-Einstein equation and intrinsic viscosity were also calculated. The low intrinsic viscosity [eta] and high Vh value of collagen in an SDS environment compared to buffer and other environments suggested a more workable system in cosmetic and dermatological preparations. The one and two-hydrogen-bonded models of this collagen in various environments have been analysed. The calculated thermodynamic parameters varied with the concentration of collagen as well as concentration of additives. The change of thermodyanamic parameters from coiled-coil to random-coil conformation upon denaturation of collagen were calculated from the amount of proline and hydroxyproline residues and compared with viscometric results. Denaturation enthalpy of the catfish collagen in buffer, SDS and urea environments has also been determined by differential scanning calorimetric (DSC) measurements, and the results are in good agreement with the viscosity-derived values. The assymmetry and molecular geometry of this collagen in buffer, SDS and urea environments are also computed. Overall, our hydrodynamic and thermodynamic results suggest that the stability of the collagen in the additive environments is in the following order: SDS > buffer > urea.

Recovering the Physical Properties of Molecular Gas in Galaxies from CO SLED Modeling

NASA Astrophysics Data System (ADS)

Kamenetzky, J.; Privon, G. C.; Narayanan, D.

2018-05-01

Modeling of the spectral line energy distribution (SLED) of the CO molecule can reveal the physical conditions (temperature and density) of molecular gas in Galactic clouds and other galaxies. Recently, the Herschel Space Observatory and ALMA have offered, for the first time, a comprehensive view of the rotational J = 4‑3 through J = 13‑12 lines, which arise from a complex, diverse range of physical conditions that must be simplified to one, two, or three components when modeled. Here we investigate the recoverability of physical conditions from SLEDs produced by galaxy evolution simulations containing a large dynamical range in physical properties. These simulated SLEDs were generally fit well by one component of gas whose properties largely resemble or slightly underestimate the luminosity-weighted properties of the simulations when clumping due to nonthermal velocity dispersion is taken into account. If only modeling the first three rotational lines, the median values of the marginalized parameter distributions better represent the luminosity-weighted properties of the simulations, but the uncertainties in the fitted parameters are nearly an order of magnitude, compared to approximately 0.2 dex in the “best-case” scenario of a fully sampled SLED through J = 10‑9. This study demonstrates that while common CO SLED modeling techniques cannot reveal the underlying complexities of the molecular gas, they can distinguish bulk luminosity-weighted properties that vary with star formation surface densities and galaxy evolution, if a sufficient number of lines are detected and modeled.

A molecular scale perspective: Monte Carlo simulation for rupturing of ultra thin polymer film melts

NASA Astrophysics Data System (ADS)

Singh, Satya Pal

2017-04-01

Monte Carlo simulation has been performed to study the rupturing process of thin polymer film under strong confinement. The change in mean square displacement; pair correlation function; density distribution; average bond length and microscopic viscosity are sampled by varying the molecular interaction parameters such as the strength and the equilibrium positions of the bonding, non-bonding potentials and the sizes of the beads. The variation in mean square angular displacement χθ = [ < Δθ2 > - < Δθ>2 ] fits very well to a function of type y (t) = A + B *e-t/τ. This may help to study the viscous properties of the films and its dependence on different parameters. The ultra thin film annealed at high temperature gets ruptured and holes are created in the film mimicking spinodal dewetting. The pair correlation function and density profile reveal rich information about the equilibrium structure of the film. The strength and equilibrium bond length of finite extensible non-linear elastic potential (FENE) and non-bonding Morse potential have clear impact on microscopic rupturing of the film. The beads show Rouse or repetition motion forming rim like structures near the holes created inside the film. The higher order interaction as dipole-quadrupole may get prominence under strong confinement. The enhanced excluded volume interaction under strong confinement may overlap with the molecular dispersion forces. It can work to reorganize the molecules at the bottom of the scale and can imprint its signature in complex patterns evolved.

Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field

PubMed Central

Shinoda, Wataru; DeVane, Russell; Klein, Michael L.

2010-01-01

A new coarse-grained (CG) intermolecular force field is presented for a series of zwitterionic lipids. The model is an extension of our previous work on nonionic surfactants and is designed to reproduce experimental surface/interfacial properties as well as distribution functions from all-atom molecular dynamics (MD) simulations. Using simple functional forms, the force field parameters are optimized for multiple lipid molecules, simultaneously. The resulting CG lipid bilayers have reasonable molecular areas, chain order parameters, and elastic properties. The computed surface pressure vs. area (π-A) curve for a DPPC monolayer demonstrates a significant improvement over the previous CG models. The DPPC monolayer has a longer persistence length than a PEG lipid monolayer, exhibiting a long-lived curved monolayer surface under negative tension. The bud ejected from an oversaturated DPPC monolayer has a large bicelle-like structure, which is different from the micellar bud formed from an oversaturated PEG lipid monolayer. We have successfully observed vesicle formation during CG-MD simulations, starting from an aggregate of DMPC molecules. Depending on the aggregate size, the lipid assembly spontaneously transforms into a closed vesicle or a bicelle. None of the various intermediate structures between these extremes seem to be stable. An attempt to observe fusion of two vesicles through the application of an external adhesion force was not successful. The present CG force field also supports stable multi-lamellar DMPC vesicles. PMID:20438090

Apparent diffusion coefficient value is a strong predictor of unsuspected aggressiveness of prostate cancer before radical prostatectomy.

PubMed

Renard Penna, Raphaele; Cancel-Tassin, Geraldine; Comperat, Eva; Mozer, Pierre; Léon, Priscilla; Varinot, Justine; Roupret, Morgan; Bitker, Marc-Olivier; Lucidarme, Olivier; Cussenot, Olivier

2016-10-01

To evaluate the use of multiparametric MRI (mp MRI) parameters in order to predict prostate cancer aggressiveness as defined by pathological Gleason score or molecular markers in a cohort of patients defined with a Gleason score of 6 at biopsy. Sixty-seven men treated by radical prostatectomy (RP) for a low grade (Gleason 6) on biopsy and mp MRI before biopsy were selected. The cycle cell proliferation (CCP) score assessed by the Prolaris test and Ki-67/PTEN expression assessed by immunohistochemistry were quantified on the RP specimens. 49.25 % of the cancers were undergraded on biopsy compared to the RP specimens. Apparent diffusion coefficient (ADC) < 0.80 × 10(-3) mm(2)/s (P value 0.003), Likert score >4 (P value 0.003) and PSA density >0.15 ng/ml/cc (P value 0.035) were significantly associated with a higher RP Gleason score. Regarding molecular markers of aggressiveness, ADC < 0.80 × 10(-3) mm(2)/s and Likert score >4 were also significantly associated with a positive staining for Ki-67 (P value 0.039 and 0.01, respectively). No association was found between any analyzed MRI or clinical parameter and the CCP score. Decreasing ADC value is a stronger indicator of aggressive prostate cancer as defined by molecular markers or postsurgical histology than biopsy characteristics.

Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

PubMed

Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

2014-11-18

CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium point are reasonably close to the CCSD(T) results but sometimes slightly deviate from them because interaction energies were not particularly optimized with parameters. Nevertheless, because the electron cloud deforms when neighboring atoms/ions induce an electric field, both vdW-DF2 and PBE0-TS seem to properly reproduce the resulting change of dispersion interaction. Thus, improvements are needed in both vdW-DF2 and PBE0-TS to better describe the interaction energies, while the B97-D3 method could benefit from the incorporation of polarization-driven energy changes that show highly anisotropic behavior. Although the current DFT-D methods need further improvement, DFT-D is very useful for computer-aided molecular design. We have used these newly developed DFT-D methods to calculate the interactions between graphene and DNA nucleobases. Using DFT-D, we describe the design of molecular receptors of π-systems, graphene based electronic devices, metalloporphyrin half-metal based spintronic devices as graphene nanoribbon (GNR) analogs, and graphene based molecular electronic devices for DNA sequencing. DFT-D has also helped us understand quantum phenomena in materials and devices of π-systems including graphene.

Interpretation of cw-ESR spectra of p-methyl-thio-phenyl-nitronyl nitroxide in a nematic liquid crystalline phase.

PubMed

Collauto, Alberto; Zerbetto, Mirco; Brustolon, Marina; Polimeno, Antonino; Caneschi, Andrea; Gatteschi, Dante

2012-03-07

In this paper we report on the characterization by continuous wave electron spin resonance spectroscopy (cw-ESR) of a nitronyl nitroxide radical in a nematic phase. A detailed analysis is performed by exploiting an innovative modeling strategy alternative to the usual spectral simulation approach: most of the molecular parameters needed to calculate the spectrum are evaluated a priori and the ESR spectrum is obtained by direct application of the stochastic Liouville equation. Allowing a limited set of fitting parameters it is possible to reproduce satisfactorily ESR spectra in the temperature range 260 K-340 K including the nematic-to-isotropic phase transition (325.1 K). Our results open the way to a more quantitative understanding of the ordering and mobility of nitronyl nitroxide radicals in nanostructured environments.

Antibacterial drugs as corrosion inhibitors for bronze surfaces in acidic solutions

NASA Astrophysics Data System (ADS)

Rotaru, Ileana; Varvara, Simona; Gaina, Luiza; Muresan, Liana Maria

2014-12-01

The present study is aiming to investigate the effect of four antibiotics (amoxicillin, ciprofloxacin, doxycycline and streptomycin,) belonging to different classes of antibacterial drugs on bronze corrosion in a solution simulating an acid rain (pH 4). Due to their ability to form protective films on the metal surface, the tested antibiotics act as corrosion inhibitors for bronze. The antibiotics were tested at various concentrations in order to determine the optimal concentration range for the best corrosion inhibiting effect. In evaluating the inhibition efficiency, polarization curves, electrochemical impedance spectroscopy, SEM and XPS measurements were used. Moreover, a correlation between the inhibition efficiency of some antibacterial drugs and certain molecular parameters was determined by quantum chemical computations. Parameters like energies EHOMO and ELUMO and HOMO-LUMO energy gap were used for correlation with the corrosion data.

Optical nonlinearity of D-A-π-D and D-A-π-A type of new chalcones for potential applications in optical limiting and density functional theory studies

NASA Astrophysics Data System (ADS)

Chandra Shekhara Shetty, T.; Chidan Kumar, C. S.; Gagan Patel, K. N.; Chia, Tze Shyang; Dharmaprakash, S. M.; Ramasami, Ponnadurai; Umar, Yunusa; Chandraju, Siddegowda; Quah, Ching Kheng

2017-09-01

Two new chalcones namely, (2E)-1-(3-fluoro-4-methoxyphenyl)-3-(4-methoxyphenyl) prop-2-en-1-one and (2E)-3-(4-chlorophenyl)-1-(3-fluoro-4-methoxyphenyl)prop-2-en-1-one were synthesized and grown as single crystals by slow evaporation technique in methanol. The FTIR spectrum recorded confirms the presence of functional groups in these materials. The molecular conformation of the compounds was achieved by single crystal X-ray diffraction studies. The thermal stability of the crystals was determined from TGA/DSC curve. The third order optical nonlinearity of the chalcone compounds in DMF solution has been carried out using an Nd:YAG laser at 532 nm as the source of excitation. The nonlinear optical response was characterized by measuring the intensity dependent refractive index n2 of the medium using Z-scan technique. It is seen that the molecules exhibit a negative (defocusing) nonlinearity and large nonlinear refractive index of the order of -1.8 × 10-11 esu. The third-order nonlinearity of the studied chalcones is dominated by nonlinear refraction, which leads to strong optical limiting of laser. The result reveals that these two new chalcone molecules would be a promising material for optical limiting applications. In addition, the optimized molecular geometry, vibrational frequencies in gas, and the Molecular Electrostatic Potential (MEP) surface parameters of the two molecules were calculated using DFT/B3LYP method with 6-311++G(d,p) basis set in ground state. All the theoretical calculations were found in good agreement with experimental data.

Adiabatic perturbation theory for atoms and molecules in the low-frequency regime

NASA Astrophysics Data System (ADS)

Martiskainen, Hanna; Moiseyev, Nimrod

2017-12-01

There is an increasing interest in the photoinduced dynamics in the low frequency, ω, regime. The multiphoton absorptions by molecules in strong laser fields depend on the polarization of the laser and on the molecular structure. The unique properties of the interaction of atoms and molecules with lasers in the low-frequency regime imply new concepts and directions in strong-field light-matter interactions. Here we represent a perturbational approach for the calculations of the quasi-energy spectrum in the low-frequency regime, which avoids the construction of the Floquet operator with extremely large number of Floquet channels. The zero-order Hamiltonian in our perturbational approach is the adiabatic Hamiltonian where the atoms/molecules are exposed to a dc electric field rather than to ac-field. This is in the spirit of the first step in the Corkum three-step model. The second-order perturbation correction terms are obtained when i ℏ ω ∂/∂ τ serves as a perturbation and τ is a dimensionless variable. The second-order adiabatic perturbation scheme is found to be an excellent approach for calculating the ac-field Floquet solutions in our test case studies of a simple one-dimensional time-periodic model Hamiltonian. It is straightforward to implement the perturbation approach presented here for calculating atomic and molecular energy shifts (positions) due to the interaction with low-frequency ac-fields using high-level electronic structure methods. This is enabled since standard quantum chemistry packages allow the calculations of atomic and molecular energy shifts due to the interaction with dc-fields. In addition to the shift of the energy positions, the energy widths (inverse lifetimes) can be obtained at the same level of theory. These energy shifts are functions of the laser parameters (low frequency, intensity, and polarization).

Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

PubMed

Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoît

2012-11-13

An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US/H-REMD strategy is implemented on the basis of parallel/parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene/P with an application to a typical biomolecular calculation of general interest, namely the binding of calcium ions to the small protein Calbindin D9k. The free energy landscape associated with two order parameters, the distance between the ion and its binding pocket and the root-mean-square deviation (rmsd) of the binding pocket relative the crystal structure, was calculated using the US/H-REMD method. The results are then used to estimate the absolute binding free energy of calcium ion to Calbindin D9k. The tests demonstrate that the 2D US/H-REMD scheme greatly accelerates the configurational sampling of the binding pocket, thereby improving the convergence of the potential of mean force calculation.

Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

PubMed

Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

2017-08-22

A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

Performance of some nucleation theories with a nonsharp droplet-vapor interface.

PubMed

Napari, Ismo; Julin, Jan; Vehkamäki, Hanna

2010-10-21

Nucleation theories involving the concept of nonsharp boundary between the droplet and vapor are compared to recent molecular dynamics (MD) simulation data of Lennard-Jones vapors at temperatures above the triple point. The theories are diffuse interface theory (DIT), extended modified liquid drop-dynamical nucleation theory (EMLD-DNT), square gradient theory (SGT), and density functional theory (DFT). Particular attention is paid to thermodynamic consistency in the comparison: the applied theories either use or, with a proper parameter adjustment, result in the same values of equilibrium vapor pressure, bulk liquid density, and surface tension as the MD simulations. Realistic pressure-density correlations are also used. The best agreement between the simulated nucleation rates and calculations is obtained from DFT, SGT, and EMLD-DNT, all of which, in the studied temperature range, show deviations of less than one order of magnitude in the nucleation rate. DIT underestimates the nucleation rate by up to two orders of magnitude. DFT and SGT give the best estimate of the molecular content of the critical nuclei. Overall, at the vapor conditions of this study, all the investigated theories perform better than classical nucleation theory in predicting nucleation rates.

Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.

A quantum chemical study of molecular properties and QSPR modeling of oximes, amidoximes and hydroxamic acids with nucleophilic activity against toxic organophosphorus agents

NASA Astrophysics Data System (ADS)

Alencar Filho, Edilson B.; Santos, Aline A.; Oliveira, Boaz G.

2017-04-01

The proposal of this work includes the use of quantum chemical methods and cheminformatics strategies in order to understand the structural profile and reactivity of α-nucleophiles compounds such as oximes, amidoximes and hydroxamic acids, related to hydrolysis rate of organophosphates. Theoretical conformational study of 41 compounds were carried out through the PM3 semiempirical Hamiltonian, followed by the geometry optimization at the B3LYP/6-31+G(d,p) level of theory, complemented by Polarized Continuum Model (PCM) to simulate the aqueous environment. In line with the experimental hypothesis about hydrolytic power, the strength of the Intramolecular Hydrogen Bonds (IHBs) at light of the Bader's Quantum Theory of Atoms in Molecules (QTAIM) is related to the preferential conformations of α-nucleophiles. A set of E-Dragon descriptors (1,666) were submitted to a variable selection through Ordered Predictor Selection (OPS) algorithm. Five descriptors, including atomic charges obtained from the Natural Bond Orbitals (NBO) protocol jointly with a fragment index associated to the presence/absence of IHBs, provided a Quantitative Structure-Property Relationship (QSPR) model via Multiple Linear Regression (MLR). This model showed good validation parameters (R2 = 0.80, Qloo2 = 0.67 and Qext2 = 0.81) and allowed the identification of significant physicochemical features on the molecular scaffold in order to design compounds potentially more active against organophosphorus poisoning.

A computer model of molecular arrangement in a n-paraffinic liquid

NASA Astrophysics Data System (ADS)

Vacatello, Michele; Avitabile, Gustavo; Corradini, Paolo; Tuzi, Angela

1980-07-01

A computer model of a bulk liquid polymer was built to investigate the problem of local order. The model is made of C30 n-alkane molecules; it is not a lattice model, but it allows for a continuous variability of torsion angles and interchain distances, subject to realistic intra- and intermolecular potentials. Experimental x-ray scattering curves and radial distribution functions are well reproduced. Calculated properties like end-to-end distances, distribution of torsion angles, radial distribution functions, and chain direction correlation parameters, all indicate a random coil conformation and no tendency to form bundles of parallel chains.

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

Wood, Mitchell; Thompson, Aidan P.

The purpose of this short contribution is to report on the development of a Spectral Neighbor Analysis Potential (SNAP) for tungsten. We have focused on the characterization of elastic and defect properties of the pure material in order to support molecular dynamics simulations of plasma-facing materials in fusion reactors. A parallel genetic algorithm approach was used to efficiently search for fitting parameters optimized against a large number of objective functions. In addition, we have shown that this many-body tungsten potential can be used in conjunction with a simple helium pair potential1 to produce accurate defect formation energies for the W-Hemore » binary system.« less

Glassy dynamics of dense particle assemblies on a spherical substrate.

PubMed

Vest, Julien-Piera; Tarjus, Gilles; Viot, Pascal

2018-04-28

We study by molecular dynamics simulation a dense one-component system of particles confined on a spherical substrate. We more specifically investigate the evolution of the structural and dynamical properties of the system when changing the control parameters, the temperature and the curvature of the substrate. We find that the dynamics become glassy at low temperature, with a strong slowdown of the relaxation and the emergence of dynamical heterogeneity. The prevalent local 6-fold order is frustrated by curvature and we analyze in detail the role of the topological defects in the statics and the dynamics of the particle assembly.

Premelting, fluctuations, and coarse-graining of water-ice interfaces.

PubMed

Limmer, David T; Chandler, David

2014-11-14

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Premelting, fluctuations, and coarse-graining of water-ice interfaces

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2014-11-01

Using statistical field theory supplemented with molecular dynamics simulations, we consider premelting on the surface of ice as a generic consequence of broken hydrogen bonds at the boundary between the condensed and gaseous phases. A procedure for coarse-graining molecular configurations onto a continuous scalar order parameter field is discussed, which provides a convenient representation of the interface between locally crystal-like and locally liquid-like regions. A number of interfacial properties are straightforwardly evaluated using this procedure such as the average premelting thickness and surface tension. The temperature and system size dependence of the premelting layer thickness calculated in this way confirms the characteristic logarithmic growth expected for the scalar field theory that the system is mapped onto through coarse-graining, though remains finite due to long-ranged interactions. Finally, from explicit simulations the existence of a premelting layer is shown to be insensitive to bulk lattice geometry, exposed crystal face, and curvature.

Ab Initio Effective Rovibrational Hamiltonians for Non-Rigid Molecules via Curvilinear VMP2

NASA Astrophysics Data System (ADS)

Changala, Bryan; Baraban, Joshua H.

2017-06-01

Accurate predictions of spectroscopic constants for non-rigid molecules are particularly challenging for ab initio theory. For all but the smallest systems, ``brute force'' diagonalization of the full rovibrational Hamiltonian is computationally prohibitive, leaving us at the mercy of perturbative approaches. However, standard perturbative techniques, such as second order vibrational perturbation theory (VPT2), are based on the approximation that a molecule makes small amplitude vibrations about a well defined equilibrium structure. Such assumptions are physically inappropriate for non-rigid systems. In this talk, we will describe extensions to curvilinear vibrational Møller-Plesset perturbation theory (VMP2) that account for rotational and rovibrational effects in the molecular Hamiltonian. Through several examples, we will show that this approach provides predictions to nearly microwave accuracy of molecular constants including rotational and centrifugal distortion parameters, Coriolis coupling constants, and anharmonic vibrational and tunneling frequencies.

Ruminal paramphistomosis in cattle from northeastern Algeria: prevalence, parasite burdens and species identification

PubMed Central

Titi, Amal; Mekroud, Abdeslam; Chibat, Mohamed el Hadi; Boucheikhchoukh, Mehdi; Zein-Eddine, Rima; Djuikwo-Teukeng, Félicité F.; Vignoles, Philippe; Rondelaud, Daniel; Dreyfuss, Gilles

2014-01-01

Slaughterhouse samples were analysed over a two-year period (September 2010–August 2012) in Jijel (northeastern Algeria) in order to determine seasonal variations in the prevalence and intensity of bovine paramphistomosis in a Mediterranean climate and identify paramphistome species using molecular biology. In spring and summer, significantly higher prevalences and lower parasite burdens were noted in bull calves, thus indicating an effect of season on these parameters. In contrast, the differences among seasonal prevalences or among seasonal parasite burdens were not significant in the case of old cows. Eleven adult worms from the slaughterhouses of Jijel and three neighbouring departments (Constantine, El Tarf and Setif) were analysed using molecular markers for species identification. Two different species, Calicophoron daubneyi and C. microbothrium, were found. The presence of these two paramphistomids raises the question of their respective frequency in the definitive host and local intermediate hosts. PMID:25279553

Porous and magnetic molecularly imprinted polymers via Pickering high internal phase emulsions polymerization for selective adsorption of λ-cyhalothrin

NASA Astrophysics Data System (ADS)

Wu, Yunlong; Ma, Yue; Pan, Jianming; Gu, Runxing; Luo, Jialu

2017-03-01

A novel macroporous magnetic molecularly imprinted polymer (MMIPs) of was prepared by W/O Pickering (high internal phase emulsions) HIPEs polymerization, and then it was adopted as adsorbent for selective adsorption of λ-cyhalothrin (LC). In static conditions, adsorption capacity of LC increased rapidly in the first 60 min and reached to equilibrium in approximately 2.0 h. Excellent conformity of the second-order model confirmed the chemical nature of the interaction between the LC and imprinted sites. The fitting adsorption isotherm was a Langmuir type, and the maximum monolayer adsorption capacity at 298 K was 404.4 µmol g-1. Thermodynamic parameters suggested the specific adsorption at 298 K was an exothermic, spontaneous, and entropy decreased process. Competitive recognition studies of the MMIPs were performed with diethyl phthalate (DEP) and the structurally similar compound fenvalerate (FL), and the MMIPs, which displayed high selectivity for LC.

Synthesis, optimization, and characterization of molecularly imprinted nanoparticles

NASA Astrophysics Data System (ADS)

Rostamizadeh, Kobra; Abdollahi, Hamid; Parsajoo, Cobra

2013-04-01

Nanoparticles of molecularly imprinted polymers (MIPs) were prepared by precipitation polymerization method. Glucose was used as a template molecule. The impact of different process parameters on the preparation of nanoparticles was investigated in order to reach the maximum binding capacity of MIPs. Experimental data based on uniform design were analyzed using artificial neural network to find the optimal condition. The results showed that the binding ability of nanoparticles of MIPs prepared under optimum condition was much higher than that of the corresponding non-imprinted nanoparticles (NIPs). The findings also demonstrated high glucose selectivity of imprinted nanoparticles. The results exhibited that the particle size for MIP nanoparticles was about 557.6 nm, and the Brunauer-Emmett-Teller analysis also confirmed that the particle pores were mesopores and macropores around 40 nm and possessed higher volume, surface area, and uniform size compared to the corresponding NIPs.

Porous and Magnetic Molecularly Imprinted Polymers via Pickering High Internal Phase Emulsions Polymerization for Selective Adsorption of λ-Cyhalothrin.

PubMed

Wu, Yunlong; Ma, Yue; Pan, Jianming; Gu, Runxing; Luo, Jialu

2017-01-01

A novel macroporous magnetic molecularly imprinted polymer (MMIPs) of was prepared by W/O Pickering (high internal phase emulsions) HIPEs polymerization, and then it was adopted as adsorbent for selective adsorption of λ-cyhalothrin (LC). In static conditions, adsorption capacity of LC increased rapidly in the first 60 min and reached to equilibrium in ~2.0 h. Excellent conformity of the second-order model confirmed the chemical nature of the interaction between the LC and imprinted sites. The fitting adsorption isotherm was a Langmuir type, and the maximum monolayer adsorption capacity at 298 K was 404.4 μmol g -1 . Thermodynamic parameters suggested the specific adsorption at 298 K was an exothermic, spontaneous, and entropy decreased process. Competitive recognition studies of the MMIPs were performed with diethyl phthalate (DEP) and the structurally similar compound fenvalerate (FL), and the MMIPs, which displayed high selectivity for LC.

Porous and Magnetic Molecularly Imprinted Polymers via Pickering High Internal Phase Emulsions Polymerization for Selective Adsorption of λ-Cyhalothrin

PubMed Central

Wu, Yunlong; Ma, Yue; Pan, Jianming; Gu, Runxing; Luo, Jialu

2017-01-01

A novel macroporous magnetic molecularly imprinted polymer (MMIPs) of was prepared by W/O Pickering (high internal phase emulsions) HIPEs polymerization, and then it was adopted as adsorbent for selective adsorption of λ-cyhalothrin (LC). In static conditions, adsorption capacity of LC increased rapidly in the first 60 min and reached to equilibrium in ~2.0 h. Excellent conformity of the second-order model confirmed the chemical nature of the interaction between the LC and imprinted sites. The fitting adsorption isotherm was a Langmuir type, and the maximum monolayer adsorption capacity at 298 K was 404.4 μmol g−1. Thermodynamic parameters suggested the specific adsorption at 298 K was an exothermic, spontaneous, and entropy decreased process. Competitive recognition studies of the MMIPs were performed with diethyl phthalate (DEP) and the structurally similar compound fenvalerate (FL), and the MMIPs, which displayed high selectivity for LC. PMID:28401145

Theoretical investigation of the molecular structure of the isoquercitrin molecule

NASA Astrophysics Data System (ADS)

Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

1999-09-01

Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

Dynamic anomalies in a supercooled liquid: a molecular dynamics study

NASA Astrophysics Data System (ADS)

Wahnström, Göran

1991-07-01

Molecular-dynamics simulations have been carried out on a two-component Lennard-Jones system, quenched into supercooled and amorphous states. Careful attention is paid to proper equilibration of the system in the supercooled liquid regime and long production runs are performed in order to reveal slow structural relaxation processes. The results for the time-dependence of the self-part of the density autocorrelation function Fqs(t) show two different slow relaxation processes, where the slowest (α relaxation) can be represented by a stretched exponential, A exp[- (t/τrel)ß]. In frequency domain this gives rise to a quasi-elastic peak and it is found that its area, the nonergodicity parameter fqs, shows an anomalous decrease when increasing the temperature towards a critical value Tc. This happens in the supercooled liquid regime and it is one of the basic predictions of the recent mode-coupling theory for the liquid-glass transition problem.

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

Molecular dynamic heterogeneity of confined lipid films by 1H magnetization-exchange nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Buda, A.; Demco, D. E.; Jagadeesh, B.; Blümich, B.

2005-01-01

The molecular dynamic heterogeneity of monolayer to submonolayer thin lecithin films confined to submicron cylindrical pores were investigated by 1H magnetization exchange nuclear magnetic resonance. In this experiment a z-magnetization gradient was generated by a double-quantum dipolar filter. The magnetization-exchange decay and buildup curves were interpreted with the help of a theoretical model based on the approximation of a one-dimensional spin-diffusion process in a three-domain morphology. The dynamic heterogeneity of the fatty acid chains and the effects of the surface area per molecule, the diameter of the pores, and the temperature were characterized with the help of local spin-diffusion coefficients. The effect of various parameters on the molecular dynamics of the mobile region of the fatty acid chains was quantified by introducing an ad hoc Gaussian distribution function of the 1H residual dipolar couplings. For the lipid films investigated in this study, the surface induced order and the geometrical confinement affect the chain dynamics of the entire molecule. Therefore, each part of the chain independently reflects the effect of surface coverage, pore size, and temperature.

Experimental and theoretical investigations on the EPR parameters and molecular orbital bonding coefficients of VO2+ ions in BTTB glasses

NASA Astrophysics Data System (ADS)

Srinivas, B.; Hameed, Abdul; Vijaya Kumar, R.; Narasimha Chary, M.; Shareefuddin, Md.

2018-06-01

The effect of the spin probe VO2+ in 15BaO-15TeO2-10TiO2-(60-x) B2O3-xV2O5 (x = 0.2, 0.4, 0.6, 0.8 mol %) glasses has been studied by employing Electron Paramagnetic Resonance (EPR) and optical absorption spectroscopic techniques. The observed EPR spectra of VO2+ ions were attributed on the basis of well-known spin-Hamiltonian of C4V symmetry. The simulated EPR spectra for VO2+ ions in the present glass system were drawn using Easy spin software. Both the experimental and simulated spectra were found to be in good agreement with each other. The optical absorption spectra exhibited three d-d transition bands due to crystal and tetragonal fields of VO2+ ions. These bands were assigned to 2B2g→ 2Eg, 2B2g→ 2B1g and 2B2g→ 2A1g transitions. The crystal field parameters Dq, Ds and Dt values are calculated. From the EPR and optical data, the molecular bonding coefficients were evaluated. Employing the higher order perturbation formulae of the g factors for 3d1 ion under tetragonally compressed octahedral fields, theoretical studies were carried out. The spin-Hamiltonian parameters ? and ? obtained from both the experimental and theoretical methods were in good agreement with each other.

Reduced Crystallization Temperature Methodology for Polymer Selection in Amorphous Solid Dispersions: Stability Perspective.

PubMed

Bhugra, Chandan; Telang, Chitra; Schwabe, Robert; Zhong, Li

2016-09-06

API-polymer interactions, used to select the right polymeric matrix with an aim to stabilize an amorphous dispersion, are routinely studied using spectroscopic and/or calorimetric techniques (i.e., melting point depression). An alternate selection tool has been explored to rank order polymers for formation of stable amorphous dispersions as a pragmatic method for polymer selection. Reduced crystallization temperature of API, a parameter introduced by Zhou et al.,1 was utilized in this study for rank ordering interactions in API-polymeric systems. The trends in reduced crystallization temperature monitored over polymer concentration range of up to 20% polymer loading were utilized to calculate "crystallization parameter" or CP for two model systems (nifedipine and BI ABC). The rank order of CP, i.e., a measure of API-polymer interaction, for nifedipine followed the order PVP > PVP-VA > Soluplus > HPMCAS > PV Ac > PAA. This rank ordering was correlated to published results of molecular interactions and physical stability for nifedipine. A different rank ordering was observed for BI ABC: PAA > PVP > HPMCAS > Soluplus > PVPV-VA > PVAc. Interactions for BI ABC were not as differentiated when compared to nifedipine based on CP trends. BI ABC dispersions at drug loadings between 40 and 60% were physically stable for prolonged periods under ICH conditions as well as accelerated stress. We propose that large CP differences among polymers could be predictive of stability outcomes. Acceptable stability at pharmaceutically relevant drug loadings would suggest that the relative influence of downstream processes, such as polymer solubility in various solvents, process suitability and selection, and more importantly supersaturation potential, should be higher compared to stability considerations while developing compounds like BI ABC.

Phase behavior of Langmuir monolayers with ionic molecular heads: Molecular simulations

NASA Astrophysics Data System (ADS)

González-Castro, Carlos A.; Ramírez-Santiago, Guillermo

2015-03-01

We carried out Monte Carlo simulations in the N ,Π,T ensemble of a Langmuir monolayer coarse-grained molecular model. Considering that the hydrophilic groups can be ionized by modulating acid-base interactions, here we study the phase behavior of a model that incorporates the short-range steric and long-range ionic interactions. The simulations were carried out in the reduced temperature range 0.1 ≤T*<4.0 , where there is a competition of these interactions. Different order parameters were calculated and analyzed for several values of the reduced surface pressure in the interval, 1 ≤Π*≤40. For most of the surface pressures two directions of molecular tilt were found: (i) towards the nearest neighbor (NN) at low temperatures, T*<0.7, and most of the values of Π* and (ii) towards next-nearest neighbors (NNN) in the temperature interval 0.7 ≤T*<1.1 for Π*<25. We also found the coexistence of the NN and NNN at intermediate temperatures and Π*>25 . A low-temperature reentrant disorder-order-disorder transition in the positions of the molecular heads and in the collective tilt of the tails was found for all the surface pressure values. It was also found that the molecular tails arranged forming "rotating patterns" in the temperature interval, 0.5

Inverse modeling for seawater intrusion in coastal aquifers: Insights about parameter sensitivities, variances, correlations and estimation procedures derived from the Henry problem

USGS Publications Warehouse

Sanz, E.; Voss, C.I.

2006-01-01

Inverse modeling studies employing data collected from the classic Henry seawater intrusion problem give insight into several important aspects of inverse modeling of seawater intrusion problems and effective measurement strategies for estimation of parameters for seawater intrusion. Despite the simplicity of the Henry problem, it embodies the behavior of a typical seawater intrusion situation in a single aquifer. Data collected from the numerical problem solution are employed without added noise in order to focus on the aspects of inverse modeling strategies dictated by the physics of variable-density flow and solute transport during seawater intrusion. Covariances of model parameters that can be estimated are strongly dependent on the physics. The insights gained from this type of analysis may be directly applied to field problems in the presence of data errors, using standard inverse modeling approaches to deal with uncertainty in data. Covariance analysis of the Henry problem indicates that in order to generally reduce variance of parameter estimates, the ideal places to measure pressure are as far away from the coast as possible, at any depth, and the ideal places to measure concentration are near the bottom of the aquifer between the center of the transition zone and its inland fringe. These observations are located in and near high-sensitivity regions of system parameters, which may be identified in a sensitivity analysis with respect to several parameters. However, both the form of error distribution in the observations and the observation weights impact the spatial sensitivity distributions, and different choices for error distributions or weights can result in significantly different regions of high sensitivity. Thus, in order to design effective sampling networks, the error form and weights must be carefully considered. For the Henry problem, permeability and freshwater inflow can be estimated with low estimation variance from only pressure or only concentration observations. Permeability, freshwater inflow, solute molecular diffusivity, and porosity can be estimated with roughly equivalent confidence using observations of only the logarithm of concentration. Furthermore, covariance analysis allows a logical reduction of the number of estimated parameters for ill-posed inverse seawater intrusion problems. Ill-posed problems may exhibit poor estimation convergence, have a non-unique solution, have multiple minima, or require excessive computational effort, and the condition often occurs when estimating too many or co-dependent parameters. For the Henry problem, such analysis allows selection of the two parameters that control system physics from among all possible system parameters. ?? 2005 Elsevier Ltd. All rights reserved.

Classical nucleation theory of homogeneous freezing of water: thermodynamic and kinetic parameters.

PubMed

Ickes, Luisa; Welti, André; Hoose, Corinna; Lohmann, Ulrike

2015-02-28

The probability of homogeneous ice nucleation under a set of ambient conditions can be described by nucleation rates using the theoretical framework of Classical Nucleation Theory (CNT). This framework consists of kinetic and thermodynamic parameters, of which three are not well-defined (namely the interfacial tension between ice and water, the activation energy and the prefactor), so that any CNT-based parameterization of homogeneous ice formation is less well-constrained than desired for modeling applications. Different approaches to estimate the thermodynamic and kinetic parameters of CNT are reviewed in this paper and the sensitivity of the calculated nucleation rate to the choice of parameters is investigated. We show that nucleation rates are very sensitive to this choice. The sensitivity is governed by one parameter - the interfacial tension between ice and water, which determines the energetic barrier of the nucleation process. The calculated nucleation rate can differ by more than 25 orders of magnitude depending on the choice of parameterization for this parameter. The second most important parameter is the activation energy of the nucleation process. It can lead to a variation of 16 orders of magnitude. By estimating the nucleation rate from a collection of droplet freezing experiments from the literature, the dependence of these two parameters on temperature is narrowed down. It can be seen that the temperature behavior of these two parameters assumed in the literature does not match with the predicted nucleation rates from the fit in most cases. Moreover a comparison of all possible combinations of theoretical parameterizations of the dominant two free parameters shows that one combination fits the fitted nucleation rates best, which is a description of the interfacial tension coming from a molecular model [Reinhardt and Doye, J. Chem. Phys., 2013, 139, 096102] in combination with the activation energy derived from self-diffusion measurements [Zobrist et al., J. Phys. Chem. C, 2007, 111, 2149]. However, some fundamental understanding of the processes is still missing. Further research in future might help to tackle this problem. The most important questions, which need to be answered to constrain CNT, are raised in this study.

Bottled SAFT: A Web App Providing SAFT-γ Mie Force Field Parameters for Thousands of Molecular Fluids.

PubMed

Ervik, Åsmund; Mejía, Andrés; Müller, Erich A

2016-09-26

Coarse-grained molecular simulation has become a popular tool for modeling simple and complex fluids alike. The defining aspects of a coarse grained model are the force field parameters, which must be determined for each particular fluid. Because the number of molecular fluids of interest in nature and in engineering processes is immense, constructing force field parameter tables by individually fitting to experimental data is a futile task. A step toward solving this challenge was taken recently by Mejía et al., who proposed a correlation that provides SAFT-γ Mie force field parameters for a fluid provided one knows the critical temperature, the acentric factor and a liquid density, all relatively accessible properties. Building on this, we have applied the correlation to more than 6000 fluids, and constructed a web application, called "Bottled SAFT", which makes this data set easily searchable by CAS number, name or chemical formula. Alternatively, the application allows the user to calculate parameters for components not present in the database. Once the intermolecular potential has been found through Bottled SAFT, code snippets are provided for simulating the desired substance using the "raaSAFT" framework, which leverages established molecular dynamics codes to run the simulations. The code underlying the web application is written in Python using the Flask microframework; this allows us to provide a modern high-performance web app while also making use of the scientific libraries available in Python. Bottled SAFT aims at taking the complexity out of obtaining force field parameters for a wide range of molecular fluids, and facilitates setting up and running coarse-grained molecular simulations. The web application is freely available at http://www.bottledsaft.org . The underlying source code is available on Bitbucket under a permissive license.

Searching the Force Field Electrostatic Multipole Parameter Space.

PubMed

Jakobsen, Sofie; Jensen, Frank

2016-04-12

We show by tensor decomposition analyses that the molecular electrostatic potential for amino acid peptide models has an effective rank less than twice the number of atoms. This rank indicates the number of parameters that can be derived from the electrostatic potential in a statistically significant way. Using this as a guideline, we investigate different strategies for deriving a reduced set of atomic charges, dipoles, and quadrupoles capable of reproducing the reference electrostatic potential with a low error. A full combinatorial search of selected parameter subspaces for N-methylacetamide and a cysteine peptide model indicates that there are many different parameter sets capable of providing errors close to that of the global minimum. Among the different reduced multipole parameter sets that have low errors, there is consensus that atoms involved in π-bonding require higher order multipole moments. The possible correlation between multipole parameters is investigated by exhaustive searches of combinations of up to four parameters distributed in all possible ways on all possible atomic sites. These analyses show that there is no advantage in considering combinations of multipoles compared to a simple approach where the importance of each multipole moment is evaluated sequentially. When combined with possible weighting factors related to the computational efficiency of each type of multipole moment, this may provide a systematic strategy for determining a computational efficient representation of the electrostatic component in force field calculations.

Thermodynamic scaling of dynamics in polymer melts: predictions from the generalized entropy theory.

PubMed

Xu, Wen-Sheng; Freed, Karl F

2013-06-21

Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ρ(γ)∕T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ~50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain rigidity, cohesive energy, chain length, and the side group length are all found to significantly affect the magnitude of the scaling exponent, and the computed trends agree well with available experiments. The variations of γ with these molecular parameters are explained by establishing a correlation between the computed molecular dependence of the scaling exponent and the fragility. Thus, the efficiency of packing the polymers is established as the universal physical mechanism determining both the fragility and the scaling exponent γ.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

PubMed

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

2017-03-27

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions.

PubMed

Pendrill, Robert; Engström, Olof; Volpato, Andrea; Zerbetto, Mirco; Polimeno, Antonino; Widmalm, Göran

2016-01-28

The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

Comparative studies on structures, mechanical properties, sensitivity, stabilities and detonation performance of CL-20/TNT cocrystal and composite explosives by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-09-19

To investigate and compare the differences of structures and properties of CL-20/TNT cocrystal and composite explosives, the CL-20/TNT cocrystal and composite models were established. Molecular dynamics simulations were performed to investigate the structures, mechanical properties, sensitivity, stabilities and detonation performance of cocrystal and composite models with COMPASS force field in NPT ensemble. The lattice parameters, mechanical properties, binding energies, interaction energy of trigger bond, cohesive energy density and detonation parameters were determined and compared. The results show that, compared with pure CL-20, the rigidity and stiffness of cocrystal and composite models decreased, while plastic properties and ductility increased, so mechanical properties can be effectively improved by adding TNT into CL-20 and the cocrystal model has better mechanical properties. The interaction energy of the trigger bond and the cohesive energy density is in the order of CL-20/TNT cocrystal > CL-20/TNT composite > pure CL-20, i.e., cocrystal model is less sensitive than CL-20 and the composite model, and has the best safety parameters. Binding energies show that the cocrystal model has higher intermolecular interaction energy values than the composite model, thus illustrating the better stability of the cocrystal model. Detonation parameters vary as CL-20 > cocrystal > composite, namely, the energy density and power of cocrystal and composite model are weakened; however, the CL-20/TNT cocrystal explosive still has desirable energy density and detonation performance. This results presented in this paper help offer some helpful guidance to better understand the mechanism of CL-20/TNT cocrystal explosives and provide some theoretical assistance for cocrystal explosive design.

Targeted molecular investigation in patients within the clinical spectrum of Auriculocondylar syndrome.

PubMed

Romanelli Tavares, Vanessa L; Zechi-Ceide, Roseli M; Bertola, Debora R; Gordon, Christopher T; Ferreira, Simone G; Hsia, Gabriella S P; Yamamoto, Guilherme L; Ezquina, Suzana A M; Kokitsu-Nakata, Nancy M; Vendramini-Pittoli, Siulan; Freitas, Renato S; Souza, Josiane; Raposo-Amaral, Cesar A; Zatz, Mayana; Amiel, Jeanne; Guion-Almeida, Maria L; Passos-Bueno, Maria Rita

2017-04-01

Auriculocondylar syndrome, mainly characterized by micrognathia, small mandibular condyle, and question mark ears, is a rare disease segregating in an autosomal dominant pattern in the majority of the families reported in the literature. So far, pathogenic variants in PLCB4, GNAI3, and EDN1 have been associated with this syndrome. It is caused by a developmental abnormality of the first and second pharyngeal arches and it is associated with great inter- and intra-familial clinical variability, with some patients not presenting the typical phenotype of the syndrome. Moreover, only a few patients of each molecular subtype of Auriculocondylar syndrome have been reported and sequenced. Therefore, the spectrum of clinical and genetic variability is still not defined. In order to address these questions, we searched for alterations in PLCB4, GNAI3, and EDN1 in patients with typical Auriculocondylar syndrome (n = 3), Pierre Robin sequence-plus (n = 3), micrognathia with additional craniofacial malformations (n = 4), or non-specific auricular dysplasia (n = 1), which could represent subtypes of Auriculocondylar syndrome. We found novel pathogenic variants in PLCB4 only in two of three index patients with typical Auriculocondylar syndrome. We also performed a detailed comparative analysis of the patients presented in this study with those previously published, which showed that the pattern of auricular abnormality and full cheeks were associated with molecularly characterized individuals with Auriculocondylar syndrome. Finally, our data contribute to a better definition of a set of parameters for clinical classification that may be used as a guidance for geneticists ordering molecular testing for Auriculocondylar syndrome. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Hansen solubility parameters for polyethylene glycols by inverse gas chromatography.

PubMed

Adamska, Katarzyna; Voelkel, Adam

2006-11-03

Inverse gas chromatography (IGC) has been applied to determine solubility parameter and its components for nonionic surfactants--polyethylene glycols (PEG) of different molecular weight. Flory-Huggins interaction parameter (chi) and solubility parameter (delta(2)) were calculated according to DiPaola-Baranyi and Guillet method from experimentally collected retention data for the series of carefully selected test solutes. The Hansen's three-dimensional solubility parameters concept was applied to determine components (delta(d), delta(p), delta(h)) of corrected solubility parameter (delta(T)). The molecular weight and temperature of measurement influence the solubility parameter data, estimated from the slope, intercept and total solubility parameter. The solubility parameters calculated from the intercept are lower than those calculated from the slope. Temperature and structural dependences of the entopic factor (chi(S)) are presented and discussed.

Unified molecular field theory for collinear and noncollinear Heisenberg antiferromagnets

DOE PAGES

Johnston, David C.

2015-02-27

In this study, a unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility χ versus temperature T below the AF ordering temperature T N to be carried out for arbitrary Heisenberg exchange interactions J ij between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature θ p in the Curie-Weiss law is written in terms of the Jmore » ij values and T N in terms of the J ij values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S. For collinear ordering these properties are the reduced temperature t=T/T N, the ratio f = θ p/T N, and S. For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that χ(T ≤ T N) of noncollinear 120° spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S, and the reduced perpendicular field versus reduced temperature phase diagram is constructed.« less

Unified molecular field theory for collinear and noncollinear Heisenberg antiferromagnets

NASA Astrophysics Data System (ADS)

Johnston, David C.

2015-02-01

A unified molecular field theory (MFT) is presented that applies to both collinear and planar noncollinear Heisenberg antiferromagnets (AFs) on the same footing. The spins in the system are assumed to be identical and crystallographically equivalent. This formulation allows calculations of the anisotropic magnetic susceptibility χ versus temperature T below the AF ordering temperature TN to be carried out for arbitrary Heisenberg exchange interactions Ji j between arbitrary neighbors j of a given spin i without recourse to magnetic sublattices. The Weiss temperature θp in the Curie-Weiss law is written in terms of the Ji j values and TN in terms of the Ji j values and an assumed AF structure. Other magnetic and thermal properties are then expressed in terms of quantities easily accessible from experiment as laws of corresponding states for a given spin S . For collinear ordering these properties are the reduced temperature t =T /TN , the ratio f =θp/TN , and S . For planar noncollinear helical or cycloidal ordering, an additional parameter is the wave vector of the helix or cycloid. The MFT is also applicable to AFs with other AF structures. The MFT predicts that χ (T ≤TN) of noncollinear 120∘ spin structures on triangular lattices is isotropic and independent of S and T and thus clarifies the origin of this universally observed behavior. The high-field magnetization and heat capacity for fields applied perpendicular to the ordering axis (collinear AFs) and ordering plane (planar noncollinear AFs) are also calculated and expressed for both types of AF structures as laws of corresponding states for a given S , and the reduced perpendicular field versus reduced temperature phase diagram is constructed.

PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

EPA Science Inventory

The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

NASA Astrophysics Data System (ADS)

Schröder, Leif; Schmitz, Christian; Bachert, Peter

2004-12-01

Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model solutions of histidine and N-acetyl- L-aspartate (NAA) enabled the assignment of an additional signal component at δ = 8 ppm of Cs in vivo to the amide group at the peptide bond. The visibility of this proton could result from hydrogen bonding which would agree with the anticipated stronger motional restriction of Cs. Referring to the observation that all dipolar-coupled multiplets resolved in localized in vivo 1H NMR spectra of human m. gastrocnemius collapse simultaneously when the fibre structure is tilted towards the magic angle ( θ ≈ 55°), a common model for molecular confinement in muscle tissue is proposed on the basis of an interaction of the studied metabolites with myocellular membrane phospholipids.

Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking.

PubMed

Tan, Xijuan; Wang, Zhuming; Chen, Donghua; Luo, Kai; Xiong, Xunyu; Song, Zhenghua

2014-08-01

The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI-CL model of lg[(I0-I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 10(3)-10(5) L mol(-1) and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT-pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nematic-like stable glasses without equilibrium liquid crystal phases

DOE Data Explorer

Gomez, Jaritza [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Gujral, Ankit [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Huang, Chengbin [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Bishop, Camille [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; Yu, Lian [School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705-2222, USA; Ediger, Mark [Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

2017-02-01

We report the thermal and structural properties of glasses of posaconazole, a rod-like molecule, prepared using physical vapor deposition (PVD). PVD glasses of posaconazole can show substantial molecular orientation depending upon the choice of substrate temperature, Tsubstrate, during deposition.Ellipsometry and IR measurements indicate that glasses prepared at Tsubstrate very near the glass transition temperature (Tg) are highly ordered. For these posaconazole glasses, the orientation order parameter is similar to that observed in macroscopically aligned nematic liquid crystals, indicating that the molecules are mostly parallel to one another and perpendicular to the interface. To our knowledge, these are the most anisotropic glasses ever prepared by PVD from a molecule that does not form equilibrium liquid crystal phases. These results are consistent with a previously proposed mechanism in which molecular orientation in PVD glasses is inherited from the orientation present at the free surface of the equilibrium liquid. This mechanism suggests that molecular orientation at the surface of the equilibrium liquid of posaconazole is nematic-like. Posaconazole glasses can show very high kinetic stability; the isothermal transformation of a 400 nm glass into the supercooled liquid occurs via a propagating front that originates at the free surface and requires ~105 times the structural relaxation time of the liquid (τα). We also studied the kinetic stability of PVD glasses of itraconazole, which is a structurally similar molecule with equilibrium liquid crystal phases. While itraconazole glasses can be even more anisotropic than posaconazole glasses, they exhibit lower kinetic stability.

Molecular structure, FT-IR, vibrational assignments, HOMO-LUMO, MEP, NBO analysis and molecular docking study of ethyl-6-(4-chlorophenyl)-4-(4-fluorophenyl)-2-oxocyclohex-3-ene-1-carboxylate.

PubMed

Sheena Mary, Y; Yohannan Panicker, C; Sapnakumari, M; Narayana, B; Sarojini, B K; Al-Saadi, Abdulaziz A; Van Alsenoy, Christian; War, Javeed Ahmad

2015-03-05

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of ethyl-6-(4-chlorophenyl)-4-(4-fluoro-phenyl)-2-oxocyclohex-3-ene-1-carboxylate have been investigated experimentally and theoretically using Gaussian09 software. The title compound was optimized using the HF and DFT levels of theory. The geometrical parameters are in agreement with the XRD data. The stability of the molecule has been analyzed by NBO analysis. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. Molecular electrostatic potential was performed by the DFT method. As can be seen from the MEP map of the title compound, regions having the negative potential are over the electro negative atoms, the region having the positive potential are over the phenyl rings and the remaining species are surrounded by zero potential. First hyperpolarizability is calculated in order to find its role in non linear optics. The title compound binds at the active sites of both CypD and β-secretase and the molecular docking results draw the conclusion that the compound might exhibit β-secretase inhibitory activity which could be utilized for development of new anti-alzheimeric drugs with mild CypD inhibitory activity. Copyright © 2014 Elsevier B.V. All rights reserved.

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

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

Yue, Kan; Huang, Mingjun; Marson, Ryan L.

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results frommore » nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures.« less

Geometry induced sequence of nanoscale Frank–Kasper and quasicrystal mesophases in giant surfactants

PubMed Central

Yue, Kan; Huang, Mingjun; Marson, Ryan L.; He, Jinlin; Huang, Jiahao; Zhou, Zhe; Wang, Jing; Liu, Chang; Yan, Xuesheng; Wu, Kan; Guo, Zaihong; Liu, Hao; Ni, Peihong; Wesdemiotis, Chrys; Zhang, Wen-Bin; Glotzer, Sharon C.; Cheng, Stephen Z. D.

2016-01-01

Frank–Kasper (F-K) and quasicrystal phases were originally identified in metal alloys and only sporadically reported in soft materials. These unconventional sphere-packing schemes open up possibilities to design materials with different properties. The challenge in soft materials is how to correlate complex phases built from spheres with the tunable parameters of chemical composition and molecular architecture. Here, we report a complete sequence of various highly ordered mesophases by the self-assembly of specifically designed and synthesized giant surfactants, which are conjugates of hydrophilic polyhedral oligomeric silsesquioxane cages tethered with hydrophobic polystyrene tails. We show that the occurrence of these mesophases results from nanophase separation between the heads and tails and thus is critically dependent on molecular geometry. Variations in molecular geometry achieved by changing the number of tails from one to four not only shift compositional phase boundaries but also stabilize F-K and quasicrystal phases in regions where simple phases of spheroidal micelles are typically observed. These complex self-assembled nanostructures have been identified by combining X-ray scattering techniques and real-space electron microscopy images. Brownian dynamics simulations based on a simplified molecular model confirm the architecture-induced sequence of phases. Our results demonstrate the critical role of molecular architecture in dictating the formation of supramolecular crystals with “soft” spheroidal motifs and provide guidelines to the design of unconventional self-assembled nanostructures. PMID:27911786

Determination of the two methyl group orientations at vapor/acetone interface with polarization null angle method in SFG vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Hua; Gan, Wei; Wu, Bao-hua; Wu, Dan; Zhang, Zhen; Wang, Hong-fei

2005-06-01

We report a direct measurement of the orientation of the two CH 3 groups of acetone molecule at the vapor/acetone interface. The interfacial acetone molecule is found well-ordered, with one methyl group points away around 14.4° ± 1.9° and another into the bulk liquid around 102.8° ± 1.9° from the interface normal, and thus the C dbnd O group points into the bulk around 135.8° ± 1.9°. These results directly confirmed the highly ordered and even crystal like interfacial structure of the vapor/acetone interface from previous MD simulation. The general formulation and accurate determination of the orientational parameter D can be used to treat interfaces with complex molecular orientations.

Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes.

PubMed

Li, Shujuan; Schmidt, Burkhard

2015-03-21

The present work deals with molecular dynamics simulations of water confined in single-walled carbon nanotubes (CNTs), with emphasis on the proton-ordering of water and its polarization. First, the water occupancy of open-ended armchair and zigzag CNTs immersed in water under ambient NPT conditions is calculated for various water models, and for varying Lennard-Jones parameters of the water-carbon interaction. As a function of the CNT diameter, the water density displays several oscillations before converging to the bulk value. Based on these results, the water structures encapsulated in 10 nm long armchair CNTs (n,n) with 5 ≤ n ≤ 10, are investigated under NVT conditions. Inside the smallest nanotubes (n = 5, 6) highly ferroelectric (FE), quasi-one-dimensional water chains are found while inside the other CNTs water molecules assemble into single-walled ice nanotubes (INTs). There are several, near-degenerate minimum energy INT structures: single helical structures were found for 7 ≤ n ≤ 10, in all cases in FE arrangement. In addition, a double helical INT structure was found for n = 8 with an even higher polarization. Prism-like structures were found only for 8 ≤ n ≤ 10 with various FE, ferrielectric (FI), and antiferroelectric (AF, n = 9, 10) proton ordering. The coexistence of the nearly iso-energetic FE, FI, and AF INT structures separated by high barriers renders the molecular dynamics highly metastable, typically with nanosecond timescales at room temperature. Hence, the replica exchange simulation method is used to obtain populations of different INT states at finite temperatures. Many of the FE INT structures confined in low-diameter CNTs are still prevalent at room temperature. Both helix-helix and helix-prism structural transitions are detected which can be either continuous (around 470 K for n = 8) or discontinuous (at 218 K for n = 9). Also melting-like transitions are found in which the INT structures are disrupted leading to a loss of FE or FI ordering of the water orientations. Also these transitions can be either smooth (for n = 7, 8) or abrupt, first-order transitions, at T = 362 K for n = 9 and at T = 285 K for n = 10.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

PubMed Central

Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

2013-01-01

Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

Impact-parameter dependence of the energy loss of fast molecular clusters in hydrogen

NASA Astrophysics Data System (ADS)

Fadanelli, R. C.; Grande, P. L.; Schiwietz, G.

2008-03-01

The electronic energy loss of molecular clusters as a function of impact parameter is far less understood than atomic energy losses. For instance, there are no analytical expressions for the energy loss as a function of impact parameter for cluster ions. In this work, we describe two procedures to evaluate the combined energy loss of molecules: Ab initio calculations within the semiclassical approximation and the coupled-channels method using atomic orbitals; and simplified models for the electronic cluster energy loss as a function of the impact parameter, namely the molecular perturbative convolution approximation (MPCA, an extension of the corresponding atomic model PCA) and the molecular unitary convolution approximation (MUCA, a molecular extension of the previous unitary convolution approximation UCA). In this work, an improved ansatz for MPCA is proposed, extending its validity for very compact clusters. For the simplified models, the physical inputs are the oscillators strengths of the target atoms and the target-electron density. The results from these models applied to an atomic hydrogen target yield remarkable agreement with their corresponding ab initio counterparts for different angles between cluster axis and velocity direction at specific energies of 150 and 300 keV/u.

Vitrified chiral-nematic liquid crystalline films for selective reflection and circular polarization

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

Katsis, D.; Chen, P.H.M.; Mastrangelo, J.C.

Nematic and left-handed chiral-nematic liquid crystals comprising methoxybiphenylbenzoate and (S)-(-)-1-phenylethylamine pendants to a cyclohexane core were synthesized and characterized. Although pristine samples were found to be polycrystalline, thermal quenching following heating to and annealing at elevated temperatures permitted the molecular orders characteristic of liquid crystalline mesomorphism to be frozen in the glassy state. Left at room temperature for 6 months, the vitrified liquid crystalline films showed no evidence of recrystallization. An orientational order parameter of 0.65 was determined with linear dichroism of a vitrified nematic film doped with Exalite 428 at a mole fraction of 0.0025. Birefringence dispersion of amore » blank vitrified nematic film was determined using a phase-difference method complemented by Abbe refractometry. A series of vitrified chiral-nematic films were prepared to demonstrate selective reflection and circular polarization with a spectral region tunable from blue to the infrared region by varying the chemical composition. The experimentally measured circular polarization spectra were found to agree with the Good-Karali theory in which all four system parameters were determined a priori: optical birefringence, average refractive index, selective reflection wavelength, and film thickness.« less

Fast reactions of aluminum and explosive decomposition products in a post-detonation environment

NASA Astrophysics Data System (ADS)

Tappan, Bryce C.; Manner, Virginia W.; Lloyd, Joseph M.; Pemberton, Steven J.

2012-03-01

In order to determine the reaction behavior of Al in RDX or HMX/cast-cured binder formulations shortly after the passage of the detonation, a series of cylinder tests was performed on formulations comprising of varying binder systems and either 3.5 μm spherical Al or LiF (an inert salt with a similar molecular weight and density to Al). In these studies, both detonation velocity and cylinder expansion velocity are measured in order to determine exactly how and when Al contributes to the explosive event, particularly in the presence of oxidizing/energetic binders. The U.S. Army Research, Development and Engineering Laboratory at Picatinny have recently coined the term "combined effects" explosives for materials such as these; as they demonstrate both high metal pushing capability and high blast ability. This study is aimed at developing a fundamental understanding of the reaction of Al with explosives decomposition products, where both the detonation and early post-detonation environment are analyzed. Reaction rates of Al metal are investigated via comparison of predicted performance based on thermoequilibrium calculations. The detonation velocities, wall velocities, and parameters at the CJ plane are some of the parameters that will be discussed.

How wet should be the reaction coordinate for ligand unbinding?

PubMed

Tiwary, Pratyush; Berne, B J

2016-08-07

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.

How wet should be the reaction coordinate for ligand unbinding?

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; Berne, B. J.

2016-08-01

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom.

How wet should be the reaction coordinate for ligand unbinding?

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

We use a recently proposed method called Spectral Gap Optimization of Order Parameters (SGOOP) [P. Tiwary and B. J. Berne, Proc. Natl. Acad. Sci. U. S. A. 113, 2839 (2016)], to determine an optimal 1-dimensional reaction coordinate (RC) for the unbinding of a bucky-ball from a pocket in explicit water. This RC is estimated as a linear combination of the multiple available order parameters that collectively can be used to distinguish the various stable states relevant for unbinding. We pay special attention to determining and quantifying the degree to which water molecules should be included in the RC. Using SGOOP with under-sampled biased simulations, we predict that water plays a distinct role in the reaction coordinate for unbinding in the case when the ligand is sterically constrained to move along an axis of symmetry. This prediction is validated through extensive calculations of the unbinding times through metadynamics and by comparison through detailed balance with unbiased molecular dynamics estimate of the binding time. However when the steric constraint is removed, we find that the role of water in the reaction coordinate diminishes. Here instead SGOOP identifies a good one-dimensional RC involving various motional degrees of freedom. PMID:27497545

Systematic theoretical investigation of the zero-field splitting in Gd(III) complexes: Wave function and density functional approaches

NASA Astrophysics Data System (ADS)

Khan, Shehryar; Kubica-Misztal, Aleksandra; Kruk, Danuta; Kowalewski, Jozef; Odelius, Michael

2015-01-01

The zero-field splitting (ZFS) of the electronic ground state in paramagnetic ions is a sensitive probe of the variations in the electronic and molecular structure with an impact on fields ranging from fundamental physical chemistry to medical applications. A detailed analysis of the ZFS in a series of symmetric Gd(III) complexes is presented in order to establish the applicability and accuracy of computational methods using multiconfigurational complete-active-space self-consistent field wave functions and of density functional theory calculations. The various computational schemes are then applied to larger complexes Gd(III)DOTA(H2O)-, Gd(III)DTPA(H2O)2-, and Gd(III)(H2O)83+ in order to analyze how the theoretical results compare to experimentally derived parameters. In contrast to approximations based on density functional theory, the multiconfigurational methods produce results for the ZFS of Gd(III) complexes on the correct order of magnitude.

Fragile-to-strong transition in liquid silica

NASA Astrophysics Data System (ADS)

Geske, Julian; Drossel, Barbara; Vogel, Michael

2016-03-01

We investigate anomalies in liquid silica with molecular dynamics simulations and present evidence for a fragile-to-strong transition at around 3100 K-3300 K. To this purpose, we studied the structure and dynamical properties of silica over a wide temperature range, finding four indicators of a fragile-to-strong transition. First, there is a density minimum at around 3000 K and a density maximum at 4700 K. The turning point is at 3400 K. Second, the local structure characterized by the tetrahedral order parameter changes dramatically around 3000 K from a higher-ordered, lower-density phase to a less ordered, higher-density phase. Third, the correlation time τ changes from an Arrhenius behavior below 3300 K to a Vogel-Fulcher-Tammann behavior at higher temperatures. Fourth, the Stokes-Einstein relation holds for temperatures below 3000 K, but is replaced by a fractional relation above this temperature. Furthermore, our data indicate that dynamics become again simple above 5000 K, with Arrhenius behavior and a classical Stokes-Einstein relation.

Nonequilibrium Langevin dynamics: A demonstration study of shear flow fluctuations in a simple fluid

NASA Astrophysics Data System (ADS)

Belousov, Roman; Cohen, E. G. D.; Rondoni, Lamberto

2017-08-01

The present paper is based on a recent success of the second-order stochastic fluctuation theory in describing time autocorrelations of equilibrium and nonequilibrium physical systems. In particular, it was shown to yield values of the related deterministic parameters of the Langevin equation for a Couette flow in a microscopic molecular dynamics model of a simple fluid. In this paper we find all the remaining constants of the stochastic dynamics, which then is simulated numerically and compared directly with the original physical system. By using these data, we study in detail the accuracy and precision of a second-order Langevin model for nonequilibrium physical systems theoretically and computationally. We find an intriguing relation between an applied external force and cumulants of the resulting flow fluctuations. This is characterized by a linear dependence of an athermal cumulant ratio, an apposite quantity introduced here. In addition, we discuss how the order of a given Langevin dynamics can be raised systematically by introducing colored noise.

Modelling of noble anaesthetic gases and high hydrostatic pressure effects in lipid bilayers

DOE PAGES

Moskovitz, Yevgeny; Yang, Hui

2015-01-08

Our objective was to study molecular processes that might be responsible for inert gas narcosis and high-pressure nervous syndrome. The classical molecular dynamics trajectories (200 ns-long) of dioleoylphosphatidylcholine (DOPC) bilayers simulated by the Berger force field were evaluated for water and the atomic distribution of noble gases around DOPC molecules at a pressure range of 1 - 1000 bar and temperature of 310 Kelvin. Xenon and argon have been tested as model gases for general anesthetics, and neon has been investigated for distortions that are potentially responsible for neurological tremor at hyperbaric conditions. The analysis of stacked radial pair distributionmore » functions of DOPC headgroup atoms revealed the explicit solvation potential of gas molecules, which correlates with their dimensions. The orientational dynamics of water molecules at the biomolecular interface should be considered as an influential factor; while excessive solvation effects appearing in the lumen of membrane-embedded ion channels could be a possible cause of inert gas narcosis. All the noble gases tested exhibit similar patterns of the order parameter for both DOPC acyl chains, which is opposite to the patterns found for the order parameter curve at high hydrostatic pressures in intact bilayers. This finding supports the ‘critical volume’ hypothesis of anesthesia pressure reversal. The irregular lipid headgroup-water boundary observed in DOPC bilayers saturated with neon in the pressure range of 1 - 100 bar could be associated with the possible manifestation of neurological tremor at the atomic scale. The non-immobilizer neon also demonstrated the highest momentum impact on the normal component of the DOPC diffusion coefficient representing monolayers undulations rate, which indicates enhanced diffusivity, rather than atom size, as the key factor.« less

Insight into the molecular mechanism of water evaporation via the finite temperature string method.

PubMed

Musolino, Nicholas; Trout, Bernhardt L

2013-04-07

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.

Atomic approximation to the projection on electronic states in the Douglas-Kroll-Hess approach to the relativistic Kohn-Sham method.

PubMed

Matveev, Alexei V; Rösch, Notker

2008-06-28

We suggest an approximate relativistic model for economical all-electron calculations on molecular systems that exploits an atomic ansatz for the relativistic projection transformation. With such a choice, the projection transformation matrix is by definition both transferable and independent of the geometry. The formulation is flexible with regard to the level at which the projection transformation is approximated; we employ the free-particle Foldy-Wouthuysen and the second-order Douglas-Kroll-Hess variants. The (atomic) infinite-order decoupling scheme shows little effect on structural parameters in scalar-relativistic calculations; also, the use of a screened nuclear potential in the definition of the projection transformation shows hardly any effect in the context of the present work. Applications to structural and energetic parameters of various systems (diatomics AuH, AuCl, and Au(2), two structural isomers of Ir(4), and uranyl dication UO(2) (2+) solvated by 3-6 water ligands) show that the atomic approximation to the conventional second-order Douglas-Kroll-Hess projection (ADKH) transformation yields highly accurate results at substantial computational savings, in particular, when calculating energy derivatives of larger systems. The size-dependence of the intrinsic error of the ADKH method in extended systems of heavy elements is analyzed for the atomization energies of Pd(n) clusters (n

2D lattice model of a lipid bilayer: Microscopic derivation and thermodynamic exploration

NASA Astrophysics Data System (ADS)

Hakobyan, Davit; Heuer, Andreas

2017-02-01

Based on all-atom Molecular Dynamics (MD) simulations of a lipid bilayer we present a systematic mapping on a 2D lattice model. Keeping the lipid type and the chain order parameter as key variables we derive a free energy functional, containing the enthalpic interaction of adjacent lipids as well as the tail entropy. The functional form of both functions is explicitly determined for saturated and polyunsaturated lipids. By studying the lattice model via Monte Carlo simulations it is possible to reproduce the temperature dependence of the distribution of order parameters of the pure lipids, including the prediction of the gel transition. Furthermore, application to a mixture of saturated and polyunsaturated lipids yields the correct phase separation behavior at lower temperatures with a simulation time reduced by approximately 7 orders of magnitude as compared to the corresponding MD simulations. Even the time-dependence of the de-mixing is reproduced on a semi-quantitative level. Due to the generality of the approach we envisage a large number of further applications, ranging from modeling larger sets of lipids, sterols, and solvent proteins to predicting nucleation barriers for the melting of lipids. Particularly, from the properties of the 2D lattice model one can directly read off the enthalpy and entropy change of the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine gel-to-liquid transition in excellent agreement with experimental and MD results.

Membrane Perturbation Induced by Interfacially Adsorbed Peptides

PubMed Central

Zemel, Assaf; Ben-Shaul, Avinoam; May, Sylvio

2004-01-01

The structural and energetic characteristics of the interaction between interfacially adsorbed (partially inserted) α-helical, amphipathic peptides and the lipid bilayer substrate are studied using a molecular level theory of lipid chain packing in membranes. The peptides are modeled as “amphipathic cylinders” characterized by a well-defined polar angle. Assuming two-dimensional nematic order of the adsorbed peptides, the membrane perturbation free energy is evaluated using a cell-like model; the peptide axes are parallel to the membrane plane. The elastic and interfacial contributions to the perturbation free energy of the “peptide-dressed” membrane are evaluated as a function of: the peptide penetration depth into the bilayer's hydrophobic core, the membrane thickness, the polar angle, and the lipid/peptide ratio. The structural properties calculated include the shape and extent of the distorted (stretched and bent) lipid chains surrounding the adsorbed peptide, and their orientational (C-H) bond order parameter profiles. The changes in bond order parameters attendant upon peptide adsorption are in good agreement with magnetic resonance measurements. Also consistent with experiment, our model predicts that peptide adsorption results in membrane thinning. Our calculations reveal pronounced, membrane-mediated, attractive interactions between the adsorbed peptides, suggesting a possible mechanism for lateral aggregation of membrane-bound peptides. As a special case of interest, we have also investigated completely hydrophobic peptides, for which we find a strong energetic preference for the transmembrane (inserted) orientation over the horizontal (adsorbed) orientation. PMID:15189858

Enantio-selective molecular dynamics of (±)-o,p-DDT uptake and degradation in water-sediment system.

PubMed

Ali, Imran; Alharbi, Omar M L; Alothman, Zeid A; Alwarthan, Abdulrahman

2018-01-01

Enantio-selective molecular dynamics of (±)-o,p-DDT uptake and degradation in water-sediment system is described. Both uptake and degradation processes of (-)-o,p-DDT were slightly higher than (+)-o,p-DDT enantiomer. The optimized parameters for uptake were 7.0μgL -1 concentration of o,p-DDT, 60min contact time, 5.0pH, 6.0gL -1 amount of reverine sediment and 25°C temperature. The maximum degradation of both (-)- and (+)-o,p-DDT was obtained with 16 days, 0.4μgL -1 concentration of o,p-DDT, pH 7 and 35°C temperature. Both uptake and degraded process followed first order rate reaction. Thermodynamic parameters indicated exothermic nature of uptake and degradation processes. Both uptake and degradation were slightly higher for (-)-enantiomer in comparison to (+)-enantiomer of o,p-DDT. It was concluded that both uptake and degradation processes are responsible for the removal of o,p-DDT from nature but uptake plays a crucial role. The percentage degradations of (-)- and (+)-o,p-DDT were 30.1 and 29.5, respectively. This study may be useful to manage o,p-DDT contamination of our earth's ecosystem. Copyright © 2017. Published by Elsevier Inc.

Quantitative structure-cytotoxicity relationship of piperic acid amides.

PubMed

Shimada, Chiyako; Uesawa, Yoshihiro; Ishihara, Mariko; Kagaya, Hajime; Kanamoto, Taisei; Terakubo, Shigemi; Nakashima, Hideki; Takao, Koichi; Miyashiro, Takaki; Sugita, Yoshiaki; Sakagami, Hiroshi

2014-09-01

A total of 12 piperic acid amides, including piperine, were subjected to quantitative structure-activity relationship (QSAR) analysis, based on their cytotoxicity, tumor selectivity and anti-HIV activity, in order to find new biological activities. Cytotoxicity against four human oral squamous cell carcinoma (OSCC) cell lines and three human oral normal cells was determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Tumor selectivity was evaluated by the ratio of the mean 50% cytotoxic concentration (CC50) against normal oral cells to that against OSCC cell lines. Anti-HIV activity was evaluated by the ratio of the CC50 to 50% HIV infection-cytoprotective concentration (EC50). Physicochemical, structural, and quantum-chemical parameters were calculated based on the conformations optimized by LowModeMD method followed by density functional theory method. All compounds showed low-to-moderate tumor selectivity, but no anti-HIV activity. N-Piperoyldopamine ( 8: ) which has a catechol moiety, showed the highest tumor selectivity, possibly due to its unique molecular shape and electrostatic interaction, especially its largest partial equalization of orbital electronegativities and vsurf descriptors. The present study suggests that molecular shape and ability for electrostatic interaction are useful parameters for estimating the tumor selectivity of piperic acid amides. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Influence of inertia on the dielectric properties of polar liquids. Application to deoxyhemoglobin S

NASA Astrophysics Data System (ADS)

Debiais, Georges; Déjardin, Jean-Louis

1991-07-01

In this paper, we have derived oscillator relations, including inertial effects, which are an extension of the Debye relations, and have shown their interest together with their limits of application. These relations may be applied as soon as the dimensionless damping parameter γ is less than 10, and yield a lot of information on the molecular structure of the medium. We have used them in the study of an abnormal hemoglobin, termed deoxyhemoglobin S, from experimental data of dielectric constants obtained by Delalic et al. Our calculation is based upon the Kramers-Kronig method. By means of a best-fit procedure of the dispersion plots together with the Cole-Cole plots, the presence of a monomeric phase and of three main aggregates which are well characterized, is found. So, we get several stereotypes of the medium, and its time evolution is interpreted in terms of molecular parameters. We calculate the moment of inertia of these aggregates and we give the evolution of the friction coefficient ξ. We remark that the decrease of γ corresponds to an ordered array of the medium and that its limiting value equal to 1.6 is related to a gel state, in full agreement with the theoretical estimate obtained by Coffey.

Tuning Structural Properties of Biocompatible Block Copolymer Micelles by Varying Solvent Composition

NASA Astrophysics Data System (ADS)

Cooksey, Tyler; Singh, Avantika; Mai Le, Kim; Wang, Shu; Kelley, Elizabeth; He, Lilin; Vajjala Kesava, Sameer; Gomez, Enrique; Kidd, Bryce; Madsen, Louis; Robertson, Megan

The self-assembly of block copolymers into micelles when introduced to selective solvents enables a wide array of applications, ranging from drug delivery to personal care products to nanoreactors. In order to probe the assembly and dynamics of micellar systems, the structural properties and solvent uptake of biocompatible poly(ethylene oxide-b- ɛ-caprolactone) (PEO-PCL) diblock copolymers in deuterated water (D2O) / tetrahydrofuran (THFd8) mixtures were investigated using small-angle neutron scattering in combination with nuclear magnetic resonance. PEO-PCL block copolymers, of varying molecular weight yet constant block ratio, formed spherical micelles through a wide range of solvent compositions. Varying the composition from 10 to 60 % by volume THFd8\\ in D2O / THFd8 mixtures was a means of varying the core-corona interfacial tension in the micelle system. An increase in THFd8 content in the bulk solvent increased the solvent uptake within the micelle core, which was comparable for the two series, irrespective of the polymer molecular weight. Differences in the behaviors of the micelle size parameters as the solvent composition varied originated from the differing trends in aggregation number for the two micelle series. Incorporation of the known unimer content determined from NMR allowed refinement of extracted micelle parameters.

Simulation of carbohydrates, from molecular docking to dynamics in water.

PubMed

Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

2013-01-01

Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

Validation of systems biology derived molecular markers of renal donor organ status associated with long term allograft function.

PubMed

Perco, Paul; Heinzel, Andreas; Leierer, Johannes; Schneeberger, Stefan; Bösmüller, Claudia; Oberhuber, Rupert; Wagner, Silvia; Engler, Franziska; Mayer, Gert

2018-05-03

Donor organ quality affects long term outcome after renal transplantation. A variety of prognostic molecular markers is available, yet their validity often remains undetermined. A network-based molecular model reflecting donor kidney status based on transcriptomics data and molecular features reported in scientific literature to be associated with chronic allograft nephropathy was created. Significantly enriched biological processes were identified and representative markers were selected. An independent kidney pre-implantation transcriptomics dataset of 76 organs was used to predict estimated glomerular filtration rate (eGFR) values twelve months after transplantation using available clinical data and marker expression values. The best-performing regression model solely based on the clinical parameters donor age, donor gender, and recipient gender explained 17% of variance in post-transplant eGFR values. The five molecular markers EGF, CD2BP2, RALBP1, SF3B1, and DDX19B representing key molecular processes of the constructed renal donor organ status molecular model in addition to the clinical parameters significantly improved model performance (p-value = 0.0007) explaining around 33% of the variability of eGFR values twelve months after transplantation. Collectively, molecular markers reflecting donor organ status significantly add to prediction of post-transplant renal function when added to the clinical parameters donor age and gender.

Prediction of solubility parameters and miscibility of pharmaceutical compounds by molecular dynamics simulations.

PubMed

Gupta, Jasmine; Nunes, Cletus; Vyas, Shyam; Jonnalagadda, Sriramakamal

2011-03-10

The objectives of this study were (i) to develop a computational model based on molecular dynamics technique to predict the miscibility of indomethacin in carriers (polyethylene oxide, glucose, and sucrose) and (ii) to experimentally verify the in silico predictions by characterizing the drug-carrier mixtures using thermoanalytical techniques. Molecular dynamics (MD) simulations were performed using the COMPASS force field, and the cohesive energy density and the solubility parameters were determined for the model compounds. The magnitude of difference in the solubility parameters of drug and carrier is indicative of their miscibility. The MD simulations predicted indomethacin to be miscible with polyethylene oxide and to be borderline miscible with sucrose and immiscible with glucose. The solubility parameter values obtained using the MD simulations values were in reasonable agreement with those calculated using group contribution methods. Differential scanning calorimetry showed melting point depression of polyethylene oxide with increasing levels of indomethacin accompanied by peak broadening, confirming miscibility. In contrast, thermal analysis of blends of indomethacin with sucrose and glucose verified general immiscibility. The findings demonstrate that molecular modeling is a powerful technique for determining the solubility parameters and predicting miscibility of pharmaceutical compounds. © 2011 American Chemical Society

Hydrodynamic cavitation in Stokes flow of anisotropic fluids.

PubMed

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G; Sengupta, Anupam

2017-05-30

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids.

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

PubMed Central

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-01-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids. PMID:28555615

New physicochemical interpretations for the adsorption of food dyes on chitosan films using statistical physics treatment.

PubMed

Dotto, G L; Pinto, L A A; Hachicha, M A; Knani, S

2015-03-15

In this work, statistical physics treatment was employed to study the adsorption of food dyes onto chitosan films, in order to obtain new physicochemical interpretations at molecular level. Experimental equilibrium curves were obtained for the adsorption of four dyes (FD&C red 2, FD&C yellow 5, FD&C blue 2, Acid Red 51) at different temperatures (298, 313 and 328 K). A statistical physics formula was used to interpret these curves, and the parameters such as, number of adsorbed dye molecules per site (n), anchorage number (n'), receptor sites density (NM), adsorbed quantity at saturation (N asat), steric hindrance (τ), concentration at half saturation (c1/2) and molar adsorption energy (ΔE(a)) were estimated. The relation of the above mentioned parameters with the chemical structure of the dyes and temperature was evaluated and interpreted. Copyright © 2014 Elsevier Ltd. All rights reserved.

Vertical-Substrate MPCVD Epitaxial Nanodiamond Growth

DOE PAGES

Tzeng, Yan-Kai; Zhang, Jingyuan Linda; Lu, Haiyu; ...

2017-02-09

Color center-containing nanodiamonds have many applications in quantum technologies and biology. Diamondoids, molecular-sized diamonds have been used as seeds in chemical vapor deposition (CVD) growth. However, optimizing growth conditions to produce high crystal quality nanodiamonds with color centers requires varying growth conditions that often leads to ad-hoc and time-consuming, one-at-a-time testing of reaction conditions. In order to rapidly explore parameter space, we developed a microwave plasma CVD technique using a vertical, rather than horizontally oriented stage-substrate geometry. With this configuration, temperature, plasma density, and atomic hydrogen density vary continuously along the vertical axis of the substrate. Finally, this variation allowedmore » rapid identification of growth parameters that yield single crystal diamonds down to 10 nm in size and 75 nm diameter optically active center silicon-vacancy (Si-V) nanoparticles. Furthermore, this method may provide a means of incorporating a wide variety of dopants in nanodiamonds without ion irradiation damage.« less

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

Parlinski, K.; Hashi, Y.; Tsunekawa, S.

A model of lanthanum orthoniobate which possesses a ferroelastic tetragonal-monoclinic phase transition is proposed. It contains only one particle per unit cell, but it is constructed consistently with symmetry changes at the phase transition. The model parameters are chosen to reproduce the bare soft mode, degree of deformation of the tetragonal unit cell to monoclinic one, and the phase transition temperature. The ferroelastic system with free boundary conditions was simulated by the molecular dynamics technique, and the second order phase transition was reproduced. The studied annealing process shows formation of the stripe lenticular domain pattern, which has been interrupted bymore » appearance of a temporary band of perpendicularly oriented lenticular domains. The maps contain W{sup {prime}}-type domain walls whose orientations are fixed only by interplay of potential parameters and not by symmetry elements. The simulated domain pattern has the same features as those observed by transmission electron microscopy. {copyright} {ital 1997 Materials Research Society.}« less

Synthesis, spectroscopic investigation and computational study of 3-(1-(((methoxycarbonyl)oxy)imino)ethyl)-2H-chromen-2-one

NASA Astrophysics Data System (ADS)

Gokula Krishnan, K.; Sivakumar, R.; Thanikachalam, V.; Saleem, H.; Arockia doss, M.

2015-06-01

The molecular structure and vibrational modes of 3-acetylcoumarin oxime carbonate (abbreviated as 3-ACOC) have been investigated by FT-IR, FT-Raman, NMR spectra and also by computational methods using HF and B3LYP with 6-311++G(d,p) basis set. The optimized geometric parameters (bond lengths, bond angles and dihedral angles) were in good agreement with the corresponding experimental values of 3-ACOC. The calculated vibrational frequencies of normal modes from DFT method matched well with the experimental values. The complete assignments were made on the basis of the total energy distribution (TED) of the vibrational modes. NMR (1H and 13C) chemical shifts were calculated by GIAO method and the results were compared with the experimental values. The other parameters like dipole moment, polarizability, first order hyperpolarizability, zero-point vibrational energy, EHOMO, ELUMO, heat capacity and entropy have also been computed.

The crystal and molecular structure of sodium 4-(2,4,6-triisopropylbenzoyl)benzoate in terms of the photochemical behaviour of the anion.

PubMed

Konieczny, Krzysztof; Bąkowicz, Julia; Turowska-Tyrk, Ilona

2015-05-01

Contrary to the known 4-(2,4,6-triisopropylbenzoyl)benzoate salts, di-μ-aqua-bis[tetraaquasodium(I)] bis[4-(2,4,6-triisopropylbenzoyl)benzoate] dihydrate, [Na2(H2O)10](C23H27O3)2·2H2O, (1), does not undergo a photochemical Norrish-Yang reaction in the crystalline state. In order to explain this photochemical inactivity, the intermolecular interactions were analyzed by means of the Hirshfeld surface and intramolecular geometrical parameters describing the possibility of a Norrish-Yang reaction were calculated. The reasons for the behaviour of the title salt are similar crystalline environments for both the o-isopropyl groups in the anion, resulting in similar geometrical parameters and orientations, and that these interaction distances differ significantly from those found in salts where the photochemical reaction occurs.

Microscopic insights into the NMR relaxation based protein conformational entropy meter

PubMed Central

Kasinath, Vignesh; Sharp, Kim A.; Wand, A. Joshua

2013-01-01

Conformational entropy is a potentially important thermodynamic parameter contributing to protein function. Quantitative measures of conformational entropy are necessary for an understanding of its role but have been difficult to obtain. An empirical method that utilizes changes in conformational dynamics as a proxy for changes in conformational entropy has recently been introduced. Here we probe the microscopic origins of the link between conformational dynamics and conformational entropy using molecular dynamics simulations. Simulation of seven pro! teins gave an excellent correlation with measures of side-chain motion derived from NMR relaxation. The simulations show that the motion of methyl-bearing side-chains are sufficiently coupled to that of other side chains to serve as excellent reporters of the overall side-chain conformational entropy. These results tend to validate the use of experimentally accessible measures of methyl motion - the NMR-derived generalized order parameters - as a proxy from which to derive changes in protein conformational entropy. PMID:24007504

Hydrodynamic cavitation in Stokes flow of anisotropic fluids

NASA Astrophysics Data System (ADS)

Stieger, Tillmann; Agha, Hakam; Schoen, Martin; Mazza, Marco G.; Sengupta, Anupam

2017-05-01

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids.

Bond Ellipticity Alternation: An Accurate Descriptor of the Nonlinear Optical Properties of π-Conjugated Chromophores.

PubMed

Lopes, Thiago O; Machado, Daniel F Scalabrini; Risko, Chad; Brédas, Jean-Luc; de Oliveira, Heibbe C B

2018-03-15

Well-defined structure-property relationships offer a conceptual basis to afford a priori design principles to develop novel π-conjugated molecular and polymer materials for nonlinear optical (NLO) applications. Here, we introduce the bond ellipticity alternation (BEA) as a robust parameter to assess the NLO characteristics of organic chromophores and illustrate its effectiveness in the case of streptocyanines. BEA is based on the symmetry of the electron density, a physical observable that can be determined from experimental X-ray electron densities or from quantum-chemical calculations. Through comparisons to the well-established bond-length alternation and π-bond order alternation parameters, we demonstrate the generality of BEA to foreshadow NLO characteristics and underline that, in the case of large electric fields, BEA is a more reliable descriptor. Hence, this study introduces BEA as a prominent descriptor of organic chromophores of interest for NLO applications.

Insight into the theoretical and experimental studies of 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone N(4)-methyl-N(4)- phenylthiosemicarbazone - A potential NLO material

NASA Astrophysics Data System (ADS)

Sangeetha, K. G.; Aravindakshan, K. K.; Safna Hussan, K. P.

2017-12-01

The synthesis, geometrical parameters, spectroscopic studies, optimised molecular structure, vibrational analysis, Mullikan population analysis, MEP, NBO, frontier molecular orbitals and NLO effects of 1-phenyl-3-methyl-4-benzoyl-5-pyrazolone N-(4)-methyl-N-(4)-phenylthiosemicarbazone, C25H23N5OS (L1) have been communicated in this paper. A combined experimental and theoretical approach was used to explore the structure and properties of the compound. For computational studies, Gaussian 09 program was used. Starting geometry of molecule was taken from X-ray refinement data and has been optimized by using DFT (B3LYP) method with the 6-31+G (d, p) basis sets. NBO analysis gave insight into the strongly delocalized structure, responsible for the nonlinearity and hence the stability of the molecule. Frontier molecular orbitals have been defined to forecast the global reactivity descriptors of L1. The computed first-order hyperpolarizability (β) of the compound is 2 times higher than that of urea and this account for its nonlinear optical property. Simultaneously, a molecular docking study of the compound was performed using GLIDE Program. For this, three biological enzymes, histone deacetylase, ribonucleotide reductase and DNA methyl transferase, were selected as receptor molecules.

Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system.

PubMed

Riniker, Sereina; van Gunsteren, Wilfred F

2012-07-28

The use of a supra-molecular coarse-grained (CG) model for liquid water as solvent in molecular dynamics simulations of biomolecules represented at the fine-grained (FG) atomic level of modelling may reduce the computational effort by one or two orders of magnitude. However, even if the pure FG model and the pure CG model represent the properties of the particular substance of interest rather well, their application in a hybrid FG/CG system containing varying ratios of FG versus CG particles is highly non-trivial, because it requires an appropriate balance between FG-FG, FG-CG, and CG-CG energies, and FG and CG entropies. Here, the properties of liquid water are used to calibrate the FG-CG interactions for the simple-point-charge water model at the FG level and a recently proposed supra-molecular water model at the CG level that represents five water molecules by one CG bead containing two interaction sites. Only two parameters are needed to reproduce different thermodynamic and dielectric properties of liquid water at physiological temperature and pressure for various mole fractions of CG water in FG water. The parametrisation strategy for the FG-CG interactions is simple and can be easily transferred to interactions between atomistic biomolecules and CG water.

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

PubMed Central

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic. PMID:26177039

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations.

PubMed

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro

2015-01-01

Estimation of configurational entropy from molecular dynamics trajectories is a difficult task which is often performed using quasi-harmonic or histogram analysis. An entirely different approach, proposed recently, estimates local density distribution around each conformational sample by measuring the distance from its nearest neighbors. In this work we show this theoretically well grounded the method can be easily applied to estimate the entropy from conformational sampling. We consider a set of systems that are representative of important biomolecular processes. In particular: reference entropies for amino acids in unfolded proteins are obtained from a database of residues not participating in secondary structure elements;the conformational entropy of folding of β2-microglobulin is computed from molecular dynamics simulations using reference entropies for the unfolded state;backbone conformational entropy is computed from molecular dynamics simulations of four different states of the EPAC protein and compared with order parameters (often used as a measure of entropy);the conformational and rototranslational entropy of binding is computed from simulations of 20 tripeptides bound to the peptide binding protein OppA and of β2-microglobulin bound to a citrate coated gold surface. This work shows the potential of the method in the most representative biological processes involving proteins, and provides a valuable alternative, principally in the shown cases, where other approaches are problematic.

Velocity fluctuations of a heavy particle interacting with a hot and cold gas: Applications to molecular ion traps

NASA Astrophysics Data System (ADS)

Vaca, Christian; Bruinsma, Robijn; Levine, Alex J.

2014-03-01

Understanding the stochastic motion of a heavy particle in a gas of lighter ones is a classic problem in statistical mechanics. Alkemade, MacDonald, and Van Kampen (AMvK) analyzed this problem in one dimension, computing the velocity distribution function of the heavy particle in a perturbation expansion using the ratio of mass of the light to the heavy particle as a small parameter. Novel tests of this theory are now being provided by modern molecular ion traps [arXiv:1310.5190]. In such experiments, the heavy molecular ion interacts with a cold gas used for sympathetic cooling and low density hot gasses that leak into the system. Thus, the heavy ion is maintained in a complex nonequilibrium state due to its interactions with the hot and cold gasses. In this talk, we present an extension of the AMvK model appropriate to these experiments. Using new analytic and computational techniques, we explore the time-dependent velocity distribution function of the molecular ion interacting with the gasses including higher order perturbative corrections necessary to discuss the case in which the ion's mass is not significantly larger than that of the other two species. Using this analysis we address the experimental observation of non-Gaussian velocity distributions of the heavy ions.

Measuring protein dynamics in live cells: protocols and practical considerations for fluorescence fluctuation microscopy

PubMed Central

Youker, Robert T.; Teng, Haibing

2014-01-01

Abstract. Quantitative analysis of protein complex stoichiometries and mobilities are critical for elucidating the mechanisms that regulate cellular pathways. Fluorescence fluctuation spectroscopy (FFS) techniques can measure protein dynamics, such as diffusion coefficients and formation of complexes, with extraordinary precision and sensitivity. Complete calibration and characterization of the microscope instrument is necessary in order to avoid artifacts during data acquisition and to capitalize on the full capabilities of FFS techniques. We provide an overview of the theory behind FFS techniques, discuss calibration procedures, provide protocols, and give practical considerations for performing FFS experiments. One important parameter recovered from FFS measurements is the relative molecular brightness that can correlate with oligomerization. Three methods for measuring molecular brightness (fluorescence correlation spectroscopy, photon-counting histogram, and number and brightness analysis) recover similar values when measuring samples under ideal conditions in vitro. However, examples are given illustrating that these different methods used for calculating molecular brightness of fluorescent molecules in cells are not always equivalent. Methods relying on spot measurements are more prone to bleaching and movement artifacts that can lead to underestimation of brightness values. We advocate for the use of multiple FFS techniques to study molecular brightnesses to overcome and compliment limitations of individual techniques. PMID:25260867

Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA

NASA Astrophysics Data System (ADS)

Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

2018-03-01

Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH 7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 103 M- 1, which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH0) and entropy change (ΔS0) were - 63.19 kJ mol- 1 and - 141.92 J mol- 1 K- 1, indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA.

Crystallographic Determination of Molecular Parameters for K2SiF6: A Physical Chemistry Laboratory Experiment.

ERIC Educational Resources Information Center

Loehlin, James H.; Norton, Alexandra P.

1988-01-01

Describes a crystallography experiment using both diffraction-angle and diffraction-intensity information to determine the lattice constant and a lattice independent molecular parameter, while still employing standard X-ray powder diffraction techniques. Details the method, experimental details, and analysis for this activity. (CW)

Bipolar Cascade Vertical-Cavity Surface-Emitting Lasers for RF Photonic Link Applications

DTIC Science & Technology

2007-09-01

6 IV Current versus Voltage . . . . . . . . . . . . . . . . . . . . . 7 MBE Molecular Beam Epitaxy ...of carrying maximum photocur- rent. Numerous material parameters have been studied. Growth parameters for molecular beam epitaxy (MBE), metal-organic...12 MOCVD Metal-Organic Chemical Vapor Deposition . . . . . . . . . . 12 CBE Chemical Beam Epitaxy . . . . . . . . . . . . . . . . . . . . 12 LPE

Simulating Bilayers of Nonionic Surfactants with the GROMOS-Compatible 2016H66 Force Field.

PubMed

Senac, Caroline; Urbach, Wladimir; Kurtisovski, Erol; Hünenberger, Philippe H; Horta, Bruno A C; Taulier, Nicolas; Fuchs, Patrick F J

2017-10-03

Polyoxyethylene glycol alkyl ether amphiphiles (C i E j ) are important nonionic surfactants, often used for biophysical and membrane protein studies. In this work, we extensively test the GROMOS-compatible 2016H66 force field in molecular dynamics simulations involving the lamellar phase of a series of C i E j surfactants, namely C 12 E 2 , C 12 E 3 , C 12 E 4 , C 12 E 5 , and C 14 E 4 . The simulations reproduce qualitatively well the monitored structural properties and their experimental trends along the surfactant series, although some discrepancies remain, in particular in terms of the area per surfactant, the equilibrium phase of C 12 E 5 , and the order parameters of C 12 E 3 , C 12 E 4 , and C 12 E 5 . The polar head of the C i E j surfactants is highly hydrated, almost like a single polyethyleneoxide (PEO) molecule at full hydration, resulting in very compact conformations. Within the bilayer, all C i E j surfactants flip-flop spontaneously within tens of nanoseconds. Water-permeation is facilitated, and the bending rigidity is 4 to 5 times lower than that of typical phospholipid bilayers. In line with another recent theoretical study, the simulations show that the lamellar phase of C i E j contains large hydrophilic pores. These pores should be abundant in order to reproduce the comparatively low NMR order parameters. We show that their contour length is directly correlated to the order parameters, and we estimate that they should occupy approximately 7-10% of the total membrane area. Due to their highly dynamic nature (rapid flip-flops, high water permeability, observed pore formation), C i E j surfactant bilayers are found to represent surprisingly challenging systems in terms of modeling. Given this difficulty, the results presented here show that the 2016H66 parameters, optimized independently considering pure-liquid as well as polar and nonpolar solvation properties of small organic molecules, represent a good starting point for simulating these systems.

Structure-activity relationships for novel drug precursor N-substituted-6-acylbenzothiazolon derivatives: A theoretical approach

NASA Astrophysics Data System (ADS)

Sıdır, Yadigar Gülseven; Sıdır, İsa

2013-08-01

In this study, the twelve new modeled N-substituted-6-acylbenzothiazolon derivatives having analgesic analog structure have been investigated by quantum chemical methods using a lot of electronic parameters and structure-activity properties; such as molecular polarizability (α), dipole moment (μ), EHOMO, ELUMO, q-, qH+, molecular volume (Vm), ionization potential (IP), electron affinity (EA), electronegativity (χ), molecular hardness (η), molecular softness (S), electrophilic index (ω), heat of formation (HOF), molar refractivity (MR), octanol-water partition coefficient (log P), thermochemical properties (entropy (S), capacity of heat (Cv)); as to investigate activity relationships with molecular structure. The correlations of log P with Vm, MR, ω, EA, EHOMO - ELUMO (ΔE), HOF in aqueous phase, χ, μ, S, η parameters, respectively are obtained, while the linear relation of log P with IP, Cv, HOF in gas phase are not observed. The log P parameter is obtained to be depending on different properties of compounds due to their complexity.

Determination of molecular contamination performance for space chamber tests

NASA Technical Reports Server (NTRS)

Scialdone, J. J.

1973-01-01

The limitations of chamber tests with regard to the molecular contamination of a spacecraft undergoing vacuum test were examined. The molecular flow conditions existing in the chamber and the parameters dictating the degree of contamination were analyzed. Equations and graphs were developed to show the fraction of molecules returning to the spacecraft out of those emitted and to show other chamber flow parameters as a function of chamber and spacecraft surface molecular pumping and geometric configuration. Type and location of instruments required to measure the outgassing, the degree of contamination, and the returning flows are also discussed.

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

PubMed Central

Liebermeister, Wolfram; Klipp, Edda

2006-01-01

Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases. PMID:17173669

Hydration shell parameters of aqueous alcohols: THz excess absorption and packing density.

PubMed

Matvejev, V; Zizi, M; Stiens, J

2012-12-06

Solvation in water requires minimizing the perturbations in its hydrogen bonded network. Hence solutes distort water molecular motions in a surrounding domain, forming a molecule-specific hydration shell. The properties of those hydration shells impact the structure and function of the solubilized molecules, both at the single molecule and at higher order levels. The size of the hydration shell and the picoseconds time-scale water dynamics retardation are revealed by terahertz (THz) absorption coefficient measurements. Room-temperature absorption coefficient at f = 0.28 [THz] is measured as a function of alcohol concentration in aqueous methanol, ethanol, 1,2-propanol, and 1-butanol solutions. Highly diluted alcohol measurements and enhanced overall measurement accuracy are achieved with a THz absorption measurement technique of nL-volume liquids in a capillary tube. In the absorption analysis, bulk and interfacial molecular domains of water and alcohol are considered. THz ideal and excess absorption coefficients are defined in accordance with thermodynamics mixing formulations. The parameter extraction method is developed based on a THz excess absorption model and hydrated solute molecule packing density representation. First, the hydration shell size is deduced from the hydrated solute packing densities at two specific THz excess absorption nonlinearity points: at infinite alcohol dilution (IAD) and at the THz excess absorption extremum (EAE). Consequently, interfacial water and alcohol molecular domain absorptions are deduced from the THz excess absorption model. The hydration shell sizes obtained at the THz excess absorption extremum are in excellent agreement with other reports. The hydration shells of methanol, ethanol, 1- and 2-propanol consist of 13.97, 22.94, 22.99, and 31.10 water molecules, respectively. The hydration shell water absorption is on average 0.774 ± 0.028 times the bulk water absorption. The hydration shell parameters might shed light on hydration dynamics of biomolecules.

Studies on third-order nonlinear optical properties of chalcone derivatives in polymer host

NASA Astrophysics Data System (ADS)

Shettigar, Seetharam; Umesh, G.; Chandrasekharan, K.; Sarojini, B. K.; Narayana, B.

2008-04-01

In this paper we present the experimental study of the third-order nonlinear optical properties of two chalcone derivatives, viz., 1-(4-methoxyphenyl)-3-(4-butyloxyphenyl)-prop-2-en-1-one and 1-(4-methoxyphenyl)-3-(4-propyloxyphenyl)-prop-2-en-1-one in PMMA host, with the prospective of reaching a compromise between good processability and high nonlinear optical properties. The nonlinear optical properties have been investigated by Z-scan technique using 7 ns laser pulses at 532 nm. The nonlinear refractive index, nonlinear absorption coefficient, magnitude of third-order susceptibility and the coupling factor have been determined. The values obtained are of the order of 10 -14 cm 2/W, 1 cm/GW, 10 -13 esu and 0.2, respectively. The molecular second hyperpolarizability for the chalcone derivatives in polymer is of the order of 10 -31 esu. Different guest/host concentrations have also been studied. The results suggest that the nonlinear properties of the chalcones have been improved when they are used as dopants in polymer matrix. The nonlinear parameters obtained are comparable with the reported values of II-VI compound semiconductors. Hence, these chalcons are a promising class of nonlinear optical dopant materials for optical device applications.

The origin of transverse anisotropy in axially symmetric single molecule magnets.

PubMed

Barra, Anne-Laure; Caneschi, Andrea; Cornia, Andrea; Gatteschi, Dante; Gorini, Lapo; Heiniger, Leo-Philipp; Sessoli, Roberta; Sorace, Lorenzo

2007-09-05

Single-crystal high-frequency electron paramagnetic resonance spectroscopy has been employed on a truly axial single molecule magnet of formula [Mn(12)O(12)(tBu-CH(2)CO(2))16(CH(3)OH)4].CH(3)OH to investigate the origin of the transverse magnetic anisotropy, a crucial parameter that rules the quantum tunneling of the magnetization. The crystal structure, including the absolute structure of the crystal used for EPR experiments, has been fully determined and found to belong to I4 tetragonal space group. The angular dependence of the resonance fields in the crystallographic ab plane shows the presence of high-order tetragonal anisotropy and strong dependence on the MS sublevels with the second-highest-field transition being angular independent. This was rationalized including competing fourth- and sixth-order transverse parameters in a giant spin Hamiltonian which describes the magnetic anisotropy in the ground S = 10 spin state of the cluster. To establish the origin of these anisotropy terms, the experimental results have been further analyzed using a simplified multispin Hamiltonian which takes into account the exchange interactions and the single ion magnetic anisotropy of the Mn(III) centers. It has been possible to establish magnetostructural correlations with spin Hamiltonian parameters up to the sixth order. Transverse anisotropy in axial single molecule magnets was found to originate from the multispin nature of the system and from the breakdown of the strong exchange approximation. The tilting of the single-ion easy axes of magnetization with respect to the 4-fold molecular axis of the cluster plays the major role in determining the transverse anisotropy. Counterintuitively, the projections of the single ion easy axes on the ab plane correspond to hard axes of magnetization.

Chemical association in simple models of molecular and ionic fluids. III. The cavity function

NASA Astrophysics Data System (ADS)

Zhou, Yaoqi; Stell, George

1992-01-01

Exact equations which relate the cavity function to excess solvation free energies and equilibrium association constants are rederived by using a thermodynamic cycle. A zeroth-order approximation, derived previously by us as a simple interpolation scheme, is found to be very accurate if the associative bonding occurs on or near the surface of the repulsive core of the interaction potential. If the bonding radius is substantially less than the core radius, the approximation overestimates the association degree and the association constant. For binary association, the zeroth-order approximation is equivalent to the first-order thermodynamic perturbation theory (TPT) of Wertheim. For n-particle association, the combination of the zeroth-order approximation with a ``linear'' approximation (for n-particle distribution functions in terms of the two-particle function) yields the first-order TPT result. Using our exact equations to go beyond TPT, near-exact analytic results for binary hard-sphere association are obtained. Solvent effects on binary hard-sphere association and ionic association are also investigated. A new rule which generalizes Le Chatelier's principle is used to describe the three distinct forms of behaviors involving solvent effects that we find. The replacement of the dielectric-continuum solvent model by a dipolar hard-sphere model leads to improved agreement with an experimental observation. Finally, equation of state for an n-particle flexible linear-chain fluid is derived on the basis of a one-parameter approximation that interpolates between the generalized Kirkwood superposition approximation and the linear approximation. A value of the parameter that appears to be near optimal in the context of this application is obtained from comparison with computer-simulation data.

Mean-field calculations of chain packing and conformational statistics in lipid bilayers: comparison with experiments and molecular dynamics studies.

PubMed Central

Fattal, D R; Ben-Shaul, A

1994-01-01

A molecular, mean-field theory of chain packing statistics in aggregates of amphiphilic molecules is applied to calculate the conformational properties of the lipid chains comprising the hydrophobic cores of dipalmitoyl-phosphatidylcholine (DPPC), dioleoyl-phosphatidylcholine (DOPC), and palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayers in their fluid state. The central quantity in this theory, the probability distribution of chain conformations, is evaluated by minimizing the free energy of the bilayer assuming only that the segment density within the hydrophobic region is uniform (liquidlike). Using this distribution we calculate chain conformational properties such as bond orientational order parameters and spatial distributions of the various chain segments. The lipid chains, both the saturated palmitoyl (-(CH2)14-CH3) and the unsaturated oleoyl (-(CH2)7-CH = CH-(CH2)7-CH3) chains are modeled using rotational isomeric state schemes. All possible chain conformations are enumerated and their statistical weights are determined by the self-consistency equations expressing the condition of uniform density. The hydrophobic core of the DPPC bilayer is treated as composed of single (palmitoyl) chain amphiphiles, i.e., the interactions between chains originating from the same lipid headgroup are assumed to be the same as those between chains belonging to different molecules. Similarly, the DOPC system is treated as a bilayer of oleoyl chains. The POPC bilayer is modeled as an equimolar mixture of palmitoyl and oleoyl chains. Bond orientational order parameter profiles, and segment spatial distributions are calculated for the three systems above, for several values of the bilayer thickness (or, equivalently, average area/headgroup) chosen, where possible, so as to allow for comparisons with available experimental data and/or molecular dynamics simulations. In most cases the agreement between the mean-field calculations, which are relatively easy to perform, and the experimental and simulation data is very good, supporting their use as an efficient tool for analyzing a variety of systems subject to varying conditions (e.g., bilayers of different compositions or thicknesses at different temperatures). PMID:7811955

Anti AIDS drug design with the help of neural networks

NASA Astrophysics Data System (ADS)

Tetko, I. V.; Tanchuk, V. Yu.; Luik, A. I.

1995-04-01

Artificial neural networks were used to analyze and predict the human immunodefiency virus type 1 reverse transcriptase inhibitors. Training and control set included 44 molecules (most of them are well-known substances such as AZT, TIBO, dde, etc.) The biological activities of molecules were taken from literature and rated for two classes: active and inactive compounds according to their values. We used topological indices as molecular parameters. Four most informative parameters (out of 46) were chosen using cluster analysis and original input parameters' estimation procedure and were used to predict activities of both control and new (synthesized in our institute) molecules. We applied pruning network algorithm and network ensembles to obtain the final classifier and avoid chance correlation. The increasing of neural network generalization of the data from the control set was observed, when using the aforementioned methods. The prognosis of new molecules revealed one molecule as possibly active. It was confirmed by further biological tests. The compound was as active as AZT and in order less toxic. The active compound is currently being evaluated in pre clinical trials as possible drug for anti-AIDS therapy.

Expanded experimental parameter space of semiflexible polymer assemblies through programmable nanomaterials

NASA Astrophysics Data System (ADS)

Smith, David; Schuldt, Carsten; Lorenz, Jessica; Tschirner, Teresa; Moebius-Winkler, Maximilian; Kaes, Josef; Glaser, Martin; Haendler, Tina; Schnauss, Joerg

2015-03-01

Biologically evolved materials are often used as inspiration in the development of new materials as well as examinations into the underlying physical principles governing their behavior. For instance, the biopolymer constituents of the highly dynamic cellular cytoskeleton such as actin have inspired a deep understanding of soft polymer-based materials. However, the molecular toolbox provided by biological systems has been evolutionarily optimized to carry out the necessary functions of cells, and the inability modify basic properties such as biopolymer stiffness hinders a meticulous examination of parameter space. Using actin as inspiration, we circumvent these limitations using model systems assembled from programmable materials such as DNA. Nanorods with comparable, but controllable dimensions and mechanical properties as actin can be constructed from small sets of specially designed DNA strands. In entangled gels, these allow us to systematically determine the dependence of network mechanical properties on parameters such as persistence length and crosslink strength. At higher concentrations in the presence of local attractive forces, we see a transition to highly-ordered bundled and ``aster'' phases similar to those previously characterized in systems of actin or microtubules.

In vitro prediction of gastrointestinal absorption of novel β-hydroxy-β-arylalkanoic acids using PAMPA technique.

PubMed

Savić, Jelena; Dobričić, Vladimir; Nikolic, Katarina; Vladimirov, Sote; Dilber, Sanda; Brborić, Jasmina

2017-03-30

Prediction of gastrointestinal absorption of thirteen newly synthesized β-hydroxy-β-arylalkanoic acids (HAA) and ibuprofen was performed using PAMPA test. The highest values of PAMPA parameters (%T and P app ) were calculated for 1C, 1B and 2C and these parameters were significantly lower in comparison to ibuprofen. QSPR analysis was performed in order to identify molecular descriptors with the highest influence on %T and -logP app and to create models which could be used for the design of novel HAA with improved gastrointestinal absorption. Obtained results indicate that introduction of branched side chain, as well as introduction of substituents on one phenyl ring (which disturb symmetry of the molecule) could have positive impact on gastrointestinal absorption. On the basis of these results, six novel HAA were designed and PAMPA parameters %T and -logP app were predicted by use of selected QSPR models. Designed derivatives should have better gastrointestinal absorption than HAA tested in this study. Copyright © 2017 Elsevier B.V. All rights reserved.

Confinement dynamics of a semiflexible chain inside nano-spheres

NASA Astrophysics Data System (ADS)

Fathizadeh, A.; Heidari, Maziar; Eslami-Mossallam, B.; Ejtehadi, M. R.

2013-07-01

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.

Metadynamics studies of crystal nucleation

PubMed Central

Giberti, Federico; Salvalaglio, Matteo; Parrinello, Michele

2015-01-01

Crystallization processes are characterized by activated events and long timescales. These characteristics prevent standard molecular dynamics techniques from being efficiently used for the direct investigation of processes such as nucleation. This short review provides an overview on the use of metadynamics, a state-of-the-art enhanced sampling technique, for the simulation of phase transitions involving the production of a crystalline solid. In particular the principles of metadynamics are outlined, several order parameters are described that have been or could be used in conjunction with metadynamics to sample nucleation events and then an overview is given of recent metadynamics results in the field of crystal nucleation. PMID:25866662

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

Xiong, L. H.; Wang, X. D.; Yu, Q.

Temperature-dependent atomistic structure evolution of liquid gallium (Ga) has been investigated by using in situ high energy X-ray diffraction experiment and ab initio molecular dynamics simulation. Both experimental and theoretical results reveal the existence of a liquid structural change around 1000 K in liquid Ga. Below and above this temperature the liquid exhibits differences in activation energy for selfdiffusion, temperature-dependent heat capacity, coordination numbers, density, viscosity, electric resistivity and thermoelectric power, which are reflected from structural changes of the bond-orientational order parameter Q6, fraction of covalent dimers, averaged string length and local atomic packing. This finding will trigger more studiesmore » on the liquid-to-liquid crossover in metallic melts.« less

Polar stationary phases based on poly(oligo ethylene glycol)diacrylates for capillary gas chromatography

NASA Astrophysics Data System (ADS)

Shiryaeva, V. E.; Popova, T. P.; Korolev, A. A.; Kanat'eva, A. Yu.; Kurganov, A. A.

2017-08-01

New stationary phases for capillary columns in GC are synthesized and studied. The phases are prepared by depositing oligo(ethylene glycol)diacrylates on the column walls and subsequent polymerization (crosslinking) in the presence of peroxide initiators. It is shown that stationary phases based on monomers with molecular weights of 10 kDa or higher exhibit separation properties similar to those of conventional stationary phases based on polyethylene glycol (PEG); however, their thermal stability is higher because they have a higher degree of crosslinking and a more ordered structure of the crosslinked polymers than the respective parameters of phases based on native PEG.

Navigating ligand protein binding free energy landscapes: universality and diversity of protein folding and molecular recognition mechanisms

NASA Astrophysics Data System (ADS)

Verkhivker, Gennady M.; Rejto, Paul A.; Bouzida, Djamal; Arthurs, Sandra; Colson, Anthony B.; Freer, Stephan T.; Gehlhaar, Daniel K.; Larson, Veda; Luty, Brock A.; Marrone, Tami; Rose, Peter W.

2001-03-01

Thermodynamic and kinetic aspects of ligand-protein binding are studied for the methotrexate-dihydrofolate reductase system from the binding free energy profile constructed as a function of the order parameter. Thermodynamic stability of the native complex and a cooperative transition to the unique native structure suggest the nucleation kinetic mechanism at the equilibrium transition temperature. Structural properties of the transition state ensemble and the ensemble of nucleation conformations are determined by kinetic simulations of the transmission coefficient and ligand-protein association pathways. Structural analysis of the transition states and the nucleation conformations reconciles different views on the nucleation mechanism in protein folding.

Simulation study of poled low-water ionomers with different architectures

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.; Löwen, Hartmut

2011-11-01

The role of the ionomer architecture in the formation of ordered structures in poled membranes is investigated by molecular dynamics computer simulations. It is shown that the length of the sidechain Ls controls both the areal density of cylindrical aggregates Nc and the diameter of these cylinders in the poled membrane. The backbone segment length Lb tunes the average diameter Ds of cylindrical clusters and the average number of sulfonates Ns in each cluster. A simple empirical formula is noted for the dependence of the number density of induced rod-like aggregates on the sidechain length Ls within the parameter range considered in this study.

Surface density: a new parameter in the fundamental metallicity relation of star-forming galaxies

NASA Astrophysics Data System (ADS)

Hashimoto, Tetsuya; Goto, Tomotsugu; Momose, Rieko

2018-04-01

Star-forming galaxies display a close relation among stellar mass, metallicity, and star formation rate (or molecular-gas mass). This is known as the fundamental metallicity relation (FMR) (or molecular-gas FMR), and it has a profound implication on models of galaxy evolution. However, there still remains a significant residual scatter around the FMR. We show here that a fourth parameter, the surface density of stellar mass, reduces the dispersion around the molecular-gas FMR. In a principal component analysis of 29 physical parameters of 41 338 star-forming galaxies, the surface density of stellar mass is found to be the fourth most important parameter. The new 4D fundamental relation forms a tighter hypersurface that reduces the metallicity dispersion to 50 per cent of that of the molecular-gas FMR. We suggest that future analyses and models of galaxy evolution should consider the FMR in a 4D space that includes surface density. The dilution time-scale of gas inflow and the star-formation efficiency could explain the observational dependence on surface density of stellar mass.

Molecular frame photoemission by a comb of elliptical high-order harmonics: a sensitive probe of both photodynamics and harmonic complete polarization state.

PubMed

Veyrinas, K; Gruson, V; Weber, S J; Barreau, L; Ruchon, T; Hergott, J-F; Houver, J-C; Lucchese, R R; Salières, P; Dowek, D

2016-12-16

Due to the intimate anisotropic interaction between an XUV light field and a molecule resulting in photoionization (PI), molecular frame photoelectron angular distributions (MFPADs) are most sensitive probes of both electronic/nuclear dynamics and the polarization state of the ionizing light field. Consequently, they encode the complex dipole matrix elements describing the dynamics of the PI transition, as well as the three normalized Stokes parameters s 1 , s 2 , s 3 characterizing the complete polarization state of the light, operating as molecular polarimetry. The remarkable development of advanced light sources delivering attosecond XUV pulses opens the perspective to visualize the primary steps of photochemical dynamics in time-resolved studies, at the natural attosecond to few femtosecond time-scales of electron dynamics and fast nuclear motion. It is thus timely to investigate the feasibility of measurement of MFPADs when PI is induced e.g., by an attosecond pulse train (APT) corresponding to a comb of discrete high-order harmonics. In the work presented here, we report MFPAD studies based on coincident electron-ion 3D momentum imaging in the context of ultrafast molecular dynamics investigated at the PLFA facility (CEA-SLIC), with two perspectives: (i) using APTs generated in atoms/molecules as a source for MFPAD-resolved PI studies, and (ii) taking advantage of molecular polarimetry to perform a complete polarization analysis of the harmonic emission of molecules, a major challenge of high harmonic spectroscopy. Recent results illustrating both aspects are reported for APTs generated in unaligned SF 6 molecules by an elliptically polarized infrared driving field. The observed fingerprints of the elliptically polarized harmonics include the first direct determination of the complete s 1 , s 2 , s 3 Stokes vector, equivalent to (ψ, ε, P), the orientation and the signed ellipticity of the polarization ellipse, and the degree of polarization P. They are compared to so far incomplete results of XUV optical polarimetry. We finally discuss the comparison between the outcomes of photoionization and high harmonic spectroscopy for the description of molecular photodynamics.

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine.

PubMed

Sun, Tiedong; Mirzoev, Alexander; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars

2017-08-24

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex 3+ ) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex 3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex 3+ -nucleic acid interactions and CoHex 3+ -induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex 3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex 3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex 3+ . We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex 3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg 2+ does not induce DNA-DNA attraction, which is also in agreement with experiment.

The methods of optical physics as a mean of the objects’ molecular structure identification (on the base of the research of dophamine and adrenaline molecules)

NASA Astrophysics Data System (ADS)

Elkin, M. D.; Alykova, O. M.; Smirnov, V. V.; Stefanova, G. P.

2017-01-01

Structural and dynamic models of dopamine and adrenaline are proposed on the basis of ab initio quantum calculations of the geometric and electronic structure. The parameters of the adiabatic potential are determined, a vibrational states interpretation of the test compound is proposed in this work. The analysis of the molecules conformational structure of the substance is made. A method for calculating the shifts of vibrational excitation frequencies in 1,2,4-threesubstituted of benzole is presented. It is based on second order perturbation theory. A choice of method and basis for calculation of a fundamental vibrations frequencies and intensities of the bands in the IR and Raman spectra is justified. The technique for evaluation of anharmonicity with cubic and quartic force constants is described. The paper presents the results of numerical experiments, geometric parameters of molecules, such as the valence bond lengths and angles between them. We obtain the frequency of the vibrational states and values of their integrated intensities. The interpretation of vibration of conformers is given. The results are in good agreement with experimental values. Proposed frequency can be used to identify the compounds of the vibrational spectra of molecules. The calculation was performed quantum density functional method DFT/B3LYP. It is shown that this method can be used to modeling the geometrical parameters molecular and electronic structure of various substituted of benzole. It allows us to construct the structural-dynamic models of this class of compounds by numerical calculations.

Recent Advances in Fractional Laser Resurfacing: New Paradigm in Optimal Parameters and Post-Treatment Wound Care

PubMed Central

Hsiao, Francis C.; Bock, Gerald N.; Eisen, Daniel B.

2012-01-01

Background Laser plays an increasingly prominent role in skin rejuvenation. The advent of fractional photothermolysis revolutionizes its application. Microcolumns of skin are focally injured, leaving intervening normal skin to facilitate rapid wound healing and orderly tissue remodeling. The Problem Even with the popularity of fractional laser devices, we still have limited knowledge about the ideal treatment parameters and postlaser wound care. Basic/Clinical Science Advances Many clinicians believe that higher microbream energy in fractional laser devices results in better clinical outcome. Two recent studies argue against this assumption. One article demonstrates that lower fluence can induce comparable molecular changes with fewer side effects. Another study corroborates this by showing that lower-density settings produce similar clinical outcome in scar remodeling as higher-density ones, but with fewer side effects. To shed light on the optimal post-treatment wound care regimen from fractional ablative resurfacing, another paper shows that platelet-rich plasma (PRP) can reduce transepidermal water loss and skin color changes within 1 month after treatment. Clinical Care Relevance For fractional nonablative resurfacing, lower settings in fluence or density may produce similar dermal remodeling as higher settings and with a better side-effect profile. Moreover, autologous PRP appears to expedite wound healing after fractional ablative resurfacing. Conclusion Lower microbeam energy in fractional laser resurfacing produces similar molecular changes and clinical outcome with fewer side effects. The findings might portend a shift in the paradigm of treatment parameters. Autologous PRP can facilitate better wound healing, albeit modestly. Long-term follow-ups and larger studies are necessary to confirm these findings. PMID:24527307

Investigation of the interface in silica-encapsulated liposomes by combining solid state NMR and first principles calculations.

PubMed

Folliet, Nicolas; Roiland, Claire; Bégu, Sylvie; Aubert, Anne; Mineva, Tzonka; Goursot, Annick; Selvaraj, Kaliaperumal; Duma, Luminita; Tielens, Frederik; Mauri, Francesco; Laurent, Guillaume; Bonhomme, Christian; Gervais, Christel; Babonneau, Florence; Azaïs, Thierry

2011-10-26

In the context of nanomedicine, liposils (liposomes and silica) have a strong potential for drug storage and release schemes: such materials combine the intrinsic properties of liposome (encapsulation) and silica (increased rigidity, protective coating, pH degradability). In this work, an original approach combining solid state NMR, molecular dynamics, first principles geometry optimization, and NMR parameters calculation allows the building of a precise representation of the organic/inorganic interface in liposils. {(1)H-(29)Si}(1)H and {(1)H-(31)P}(1)H Double Cross-Polarization (CP) MAS NMR experiments were implemented in order to explore the proton chemical environments around the silica and the phospholipids, respectively. Using VASP (Vienna Ab Initio Simulation Package), DFT calculations including molecular dynamics, and geometry optimization lead to the determination of energetically favorable configurations of a DPPC (dipalmitoylphosphatidylcholine) headgroup adsorbed onto a hydroxylated silica surface that corresponds to a realistic model of an amorphous silica slab. These data combined with first principles NMR parameters calculations by GIPAW (Gauge Included Projected Augmented Wave) show that the phosphate moieties are not directly interacting with silanols. The stabilization of the interface is achieved through the presence of water molecules located in-between the head groups of the phospholipids and the silica surface forming an interfacial H-bonded water layer. A detailed study of the (31)P chemical shift anisotropy (CSA) parameters allows us to interpret the local dynamics of DPPC in liposils. Finally, the VASP/solid state NMR/GIPAW combined approach can be extended to a large variety of organic-inorganic hybrid interfaces.

LH/hCG-Receptor Expression May Have a Negative Prognostic Value in Low-Risk Endometrial Cancer.

PubMed

Noci, Ivo; Sorbi, Flavia; Mannini, Luca; Projetto, Elisabetta; Pillozzi, Serena; Ghizzoni, Viola; Lottini, Tiziano; Moncini, Daniela; Baroni, Gianna; Mungai, Francesco; Arcangeli, Annarosa; Fambrini, Massimiliano

2016-01-01

A 51 year-old woman was diagnosed with endometrial cancer (EC) and underwent surgical staging. Pathological evaluation showed a 2 cm × 1 cm G2 endometrioid EC with a 30% myometrial deep invasion (FIGO Stage 1A). The patient was classified as low risk of recurrence, and no adjuvant treatment was offered. Six months after surgery, the patient developed an early vescico-vaginal recurrence, and chemotherapy treatment was started. Few months later, a subsequent involvement of vaginal wall, ileum, and omentum was detected, and the patient underwent second surgery. LH/hCG-receptor (LH/hCG-R) expression has been previously reported to be associated with an invasive phenotype in EC cells. Moreover, in a preclinical mouse model of EC behaves as a prometastatic molecular device. We analyzed the expression level of LH/hCG-R in cancer specimens collected during surgeries. Molecular and immunohistochemical analyses showed a strong expression of both mRNA and protein for LH/hCG-R in all specimens. LH/hCG-R expression may be assessed together with other clinicopathological parameters in order to better predict the risk of recurrence in low-risk EC patients. Further clinical trials are warranted in order to validate LH/hCG-R as biomarker in EC.

Towards molecular modeling of the impact of heparin-derived oligosaccharides on hIFN-γ binding

NASA Astrophysics Data System (ADS)

Lilkova, E.; Petkov, P.; Ilieva, N.; Litov, L.

2015-10-01

Human interferon gamma (hIFN-γ) is an important signalling molecule, which plays a key role in the formation and modulation of immune response. The role of the cytokine C-termini in the formation of a complex with the extracellular receptor is still controversial due to the lack of structural information about this domain. Moreover, the C-termini are also responsible for the high affinity interaction of hIFN-γ with the glycosaminoglicans heparan sulfate and heparin. This interaction can drastically change the properties and behaviour of the protein. We performed molecular dynamics simulations in order to model the structure of the hIFN-γ C-terminal part and the interaction of the cytokine with heparin-derived oligosaccharides. For this purpose we reconstructed the missing C-terminal amino acid residues and performed folding simulations to determine their conformation. In order to simulate the interaction with heparin-like fragments, we developed CHARMM 36 compatible force field for the sulfamate anion group that is present in the glucosamine sugar to complete the heparin and heparan sulfate force field. The new topology and parameters reproduce the available experimental structural properties of heparin-like fragments. The simulations show that the oligosaccharides quickly bind the IFN-γ C-termini and reduce their solvent accessible surface area.

Vibrational, UV spectra, NBO, first order hyperpolarizability and HOMO-LUMO analysis of carvedilol

NASA Astrophysics Data System (ADS)

Swarnalatha, N.; Gunasekaran, S.; Nagarajan, M.; Srinivasan, S.; Sankari, G.; Ramkumaar, G. R.

2015-02-01

In this work, we have investigated experimentally and theoretically on the molecular structure, vibrational spectra, UV spectral analysis and NBO studies of cardio-protective drug carvedilol. The FT-Raman and FT-IR spectra for carvedilol in the solid phase have been recorded in the region 4000-100 cm-1 and 4000-400 cm-1 respectively. Theoretical calculations were performed by using density functional theory (DFT) method at B3LYP/6-31G(d,p) and B3LYP/6-31++G(d,p) basis set levels. The harmonic vibrational frequencies, the optimized geometric parameters have been interpreted and compared with the reported experimental values. The complete vibrational assignments were performed on the basis of potential energy distribution (PED) of the vibrational modes. The thermodynamic properties and molecular electrostatic potential surfaces of the molecule were constructed. The electronic absorption spectrum was recorded in the region 400-200 nm and electronic properties such as HOMO and LUMO energies were calculated. The stability of the molecule arising from hyper conjugative interactions and charge delocalization have been analyzed from natural bond orbital (NBO) analysis. The first order hyperpolarizability of the title molecule was also calculated. The photo stability of carvedilol under different storage conditions were analyzed using UV-Vis spectral technique.

Ultra-cold molecules in an atomic Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Wynar, Roahn Helden

2000-08-01

This thesis is about photoassociation of Bose-condensed 87Rb. Most importantly we report that state selected 87Rb2 molecules were created at rest in a condensate of 87Rb using two-photon photoassociation. Additionally, we have identified three weakly bound states of the 87Rb2 S+u3 , potential for the |1, -1> + |1, - 1> collisional channel. The binding energies of these states are 529.4 +/- .07, 636.0094 +/- .0012, and 24.24 +/- .01 MHz respectively. We have also carried out a detailed study of the density dependence of the shift and width of the two-photon lineshape. This shift and width is modeled using the theory of Bohn and Julienne [34] and in addition to the precise measurement of binding energy we also report the first measurement of an atom molecule scattering length, aam, which we conclude is -180 +/- 150 a0, and the inelastic collision rate, Kinel < 8 × 10-11 cm-3/s. Stimulated Raman free bound coupling in an atomic Bose- Einstein condensate may lead to the formation of a molecular condensate. In order to evaluate this possibility we present a many-body quantum mean field theory of a Bose-Einstein condensate that includes a density dependent coherent coupling between atoms and molecules. This theory yields two coupled equations, one for the evolution of atomic condensate amplitude and one for the evolution of molecular condensate amplitude. The nature of the atomic-molecular condensate evolution is shown to depend on six, model parameters including the coherent coupling, given by cn . The other five parameters can be interpreted as light-shifts and incoherent loss rates. We present a calculation intended to estimate the values of these six parameters for the 87Rb - 87Rb 2 system. Based on the results of this calculation we identify two locations in the 87Rb2 spectrum where coherent transfer of population from atomic condensate to molecular condensate is plausible. Finally, we examine the credibility of the theoretical model used to estimate the six parameters used by the mean field theory. By comparing the measured Stark shifts of two-color resonances with predictions based on our theoretical model we conclude that the model is satisfactory for the v = 37 level of the S+u3 potential. This work also describes the experimental details of stabilizing a Coherent 899-01 Ti:Saphire laser and the experimental methods important to executing photoassociation in a time-averaged-orbiting potential (TOP) trap.

A time correlation function theory describing static field enhanced third order optical effects at interfaces.

PubMed

Neipert, Christine; Space, Brian

2006-12-14

Sum vibrational frequency spectroscopy, a second order optical process, is interface specific in the dipole approximation. At charged interfaces, there exists a static field, and as a direct consequence, the experimentally detected signal is a combination of enhanced second and static field induced third order contributions. There is significant evidence in the literature of the importance/relative magnitude of this third order contribution, but no previous molecularly detailed approach existed to separately calculate the second and third order contributions. Thus, for the first time, a molecularly detailed time correlation function theory is derived here that allows for the second and third order contributions to sum frequency vibrational spectra to be individually determined. Further, a practical, molecular dynamics based, implementation procedure for the derived correlation functions that describe the third order phenomenon is also presented. This approach includes a novel generalization of point atomic polarizability models to calculate the hyperpolarizability of a molecular system. The full system hyperpolarizability appears in the time correlation functions responsible for third order contributions in the presence of a static field.

Spectral Line-Shape Model to Replace the Voigt Profile in Spectroscopic Databases

NASA Astrophysics Data System (ADS)

Lisak, Daniel; Ngo, Ngoc Hoa; Tran, Ha; Hartmann, Jean-Michel

2014-06-01

The standard description of molecular line shapes in spectral databases and radiative transfer codes is based on the Voigt profile. It is well known that its simplified assumptions of absorber free motion and independence of collisional parameters from absorber velocity lead to systematic errors in analysis of experimental spectra, and retrieval of gas concentration. We demonstrate1,2 that the partially correlated quadratic speed-dependent hardcollision profile3. (pCqSDHCP) is a good candidate to replace the Voigt profile in the next generations of spectroscopic databases. This profile takes into account the following physical effects: the Doppler broadening, the pressure broadening and shifting of the line, the velocity-changing collisions, the speed-dependence of pressure broadening and shifting, and correlations between velocity- and phase/state-changing collisions. The speed-dependence of pressure broadening and shifting is incorporated into the pCqSDNGP in the so-called quadratic approximation. The velocity-changing collisions lead to the Dicke narrowing effect; however in many cases correlations between velocityand phase/state-changing collisions may lead to effective reduction of observed Dicke narrowing. The hard-collision model of velocity-changing collisions is also known as the Nelkin-Ghatak model or Rautian model. Applicability of the pCqSDHCP for different molecular systems was tested on calculated and experimental spectra of such molecules as H2, O2, CO2, H2O in a wide span of pressures. For all considered systems, pCqSDHCP is able to describe molecular spectra at least an order of magnitude better than the Voigt profile with all fitted parameters being linear with pressure. In the most cases pCqSDHCP can reproduce the reference spectra down to 0.2% or better, which fulfills the requirements of the most demanding remote-sensing applications. An important advantage of pCqSDHCP is that a fast algorithm for its computation was developedab4,5 and allows for its calculation only a few times slower than the standard Voigt profile. Moreover, the pCqSDHCP reduces to many simpler models commonly used in experimental spectra analysis simply by setting some parameters to zero, and it can be easily extended to incorporate the line-mixing effect in the first-order approximation. The idea of using pCqSDHCP as a standard profile to go beyond the Voigt profile for description of H2O line shapes was recently supported by the IUPAC task group6 which also recommended to call this profile with fast computation algorithm the HTP profile (for Hartmann-Tran).

Evolution of anisotropy in bcc Fe distorted by interstitial boron

NASA Astrophysics Data System (ADS)

Gölden, Dominik; Zhang, Hongbin; Radulov, Iliya; Dirba, Imants; Komissinskiy, Philipp; Hildebrandt, Erwin; Alff, Lambert

2018-01-01

The evolution of magnetic anisotropy in bcc Fe as a function of interstitial boron atoms was investigated in thin films grown by molecular beam epitaxy. The thermodynamic nonequilibrium conditions during film growth allowed one to stabilize an interstitial boron content of about 14 at .% accompanied by lattice tetragonalization. The c /a ratio scaled linearly with the boron content up to a maximum value of 1.05 at 300 °C substrate growth temperature, with a room-temperature magnetization of. In contrast to nitrogen interstitials, the magnetic easy axis remained in-plane with an anisotropy of approximately -5.1 ×106erg /cm3 . Density functional theory calculations using the measured lattice parameters confirm this value and show that boron local ordering indeed favors in-plane magnetization. Given the increased temperature stability of boron interstitials as compared to nitrogen interstitials, this study will help to find possible ways to manipulate boron interstitials into a more favorable local order.

Control of the orientation and photoinduced phase transitions of macrocyclic azobenzene.

PubMed

Uchida, Emi; Sakaki, Kouji; Nakamura, Yumiko; Azumi, Reiko; Hirai, Yuki; Akiyama, Haruhisa; Yoshida, Masaru; Norikane, Yasuo

2013-12-16

Photoinduced phase transitions caused by photochromic reactions bring about a change in the state of matter at constant temperature. Herein, we report the photoinduced phase transitions of crystals of a photoresponsive macrocyclic compound bearing two azobenzene groups (1) at room temperature on irradiation with UV (365 nm) and visible (436 nm) light. The trans/trans isomer undergoes photoinduced phase transitions (crystal-isotropic phase-crystal) on UV light irradiation. The photochemically generated crystal exhibited reversible phase transitions between the crystal and the mesophase on UV and visible light irradiation. The molecular order of the randomly oriented crystals could be increased by irradiating with linearly polarized visible light, and the value of the order parameter was determined to be -0.84. Heating enhances the thermal cis-to-trans isomerization and subsequent cooling returned crystals of the trans/trans isomer. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural correlation of the chalcogenide Ge40Se60 glass

NASA Astrophysics Data System (ADS)

Moharram, A. H.

2017-01-01

Binary Ge40Se60 glass was prepared using the melt-quench technique. The total structure factors, S( K), are obtained using the X-ray diffraction in the wave vector interval 0.28 ≤ K ≤ 6.5 Å-1. The appearance of the first sharp diffraction peak (FSDP) in the structure factor indicates the presence of the intermediate range order. Radial distribution functions, RDF( r), have been obtained using either the conventional (Fourier) transformation or the Monte Carlo simulation of the experimental X-ray data. The short range order parameters deduced from the Monte Carlo total correlation, T( r), functions are better than those obtained from the conventional (Fourier) T( r) data. Gaussian analyses of the total correlation function show that Ge2(Se1/2)6 molecular units are the basic structural units for the investigated Ge40Se60 glass.

Spatial distribution on high-order-harmonic generation of an H2+ molecule in intense laser fields

NASA Astrophysics Data System (ADS)

Zhang, Jun; Ge, Xin-Lei; Wang, Tian; Xu, Tong-Tong; Guo, Jing; Liu, Xue-Shen

2015-07-01

High-order-harmonic generation (HHG) for the H2 + molecule in a 3-fs, 800-nm few-cycle Gaussian laser pulse combined with a static field is investigated by solving the one-dimensional electronic and one-dimensional nuclear time-dependent Schrödinger equation within the non-Born-Oppenheimer approximation. The spatial distribution in HHG is demonstrated and the results present the recombination process of the electron with the two nuclei, respectively. The spatial distribution of the HHG spectra shows that there is little possibility of the recombination of the electron with the nuclei around the origin z =0 a.u. and equilibrium internuclear positions z =±1.3 a.u. This characteristic is irrelevant to laser parameters and is only attributed to the molecular structure. Furthermore, we investigate the time-dependent electron-nuclear wave packet and ionization probability to further explain the underlying physical mechanism.

Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

NASA Astrophysics Data System (ADS)

Doi, Hideo; Okuwaki, Koji; Mochizuki, Yuji; Ozawa, Taku; Yasuoka, Kenji

2017-09-01

In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called χ parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the χ parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based χ parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results.

Modeling of adsorption isotherms of phenol and chlorophenols onto granular activated carbon. Part I. Two-parameter models and equations allowing determination of thermodynamic parameters.

PubMed

Hamdaoui, Oualid; Naffrechoux, Emmanuel

2007-08-17

The adsorption equilibrium isotherms of five phenolic compounds from aqueous solutions onto granular activated carbon (GAC) were studied and modeled. Phenol (Ph), 2-chlorophenol (2-CP), 4-chlorophenol (4-CP), 2,4-dichlorophenol (DCP), and 2,4,6-trichlorophenol (TCP) were chosen for the adsorption tests. To predict the adsorption isotherms and to determine the characteristic parameters for process design, seven isotherm models: Langmuir (five linear forms), Freundlich, Elovich, Temkin, Fowler-Guggenheim, Kiselev, and Hill-de Boer models were applied to experimental data. The results reveal that the adsorption isotherm models fitted the data in the order: Fowler-Guggenheim>Hill-de Boer>Temkin>Freundlich>Kiselev>Langmuir isotherms. Adsorption isotherms modeling shows that the interaction of phenolic compounds with activated carbon surface is localized monolayer adsorption, that is adsorbed molecules are adsorbed at definite, localized sites. Each site can accommodate only one molecule. The interaction among adsorbed molecules is repulsive and there is no association between them, adsorption is carried out on energetically different sites and is an exothermic process. Uptake of phenols increases in the order Ph<2-CP<4-CP

Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics.

PubMed

Papadakis, G; Friedt, J M; Eck, M; Rabus, D; Jobst, G; Gizeli, E

2017-09-01

The development of integrated platforms incorporating an acoustic device as the detection element requires addressing simultaneously several challenges of technological and scientific nature. The present work was focused on the design of a microfluidic module, which, combined with a dual or array type Love wave acoustic chip could be applied to biomedical applications and molecular diagnostics. Based on a systematic study we optimized the mechanics of the flow cell attachment and the sealing material so that fluidic interfacing/encapsulation would impose minimal losses to the acoustic wave. We have also investigated combinations of operating frequencies with waveguide materials and thicknesses for maximum sensitivity during the detection of protein and DNA biomarkers. Within our investigations neutravidin was used as a model protein biomarker and unpurified PCR amplified Salmonella DNA as the model genetic target. Our results clearly indicate the need for experimental verification of the optimum engineering and analytical parameters, in order to develop commercially viable systems for integrated analysis. The good reproducibility of the signal together with the ability of the array biochip to detect multiple samples hold promise for the future use of the integrated system in a Lab-on-a-Chip platform for application to molecular diagnostics.

Phase transition between quantum and classical regimes for the escape rate of dimeric molecular nanomagnets in a staggered magnetic field

NASA Astrophysics Data System (ADS)

Owerre, S. A.; Paranjape, M. B.

2014-04-01

We study the phase transition of the escape rate of exchange-coupled dimer of single-molecule magnets which are coupled either ferromagnetically or antiferromagnetically in a staggered magnetic field and an easy z-axis anisotropy. The Hamiltonian for this system has been used to study dimeric molecular nanomagnet [Mn4]2 which is comprised of two single molecule magnets coupled antiferromagnetically. We generalize the method of mapping a single-molecule magnetic spin problem onto a quantum-mechanical particle to dimeric molecular nanomagnets. The problem is mapped to a single particle quantum-mechanical Hamiltonian in terms of the relative coordinate and a coordinate dependent reduced mass. It is shown that the presence of the external staggered magnetic field creates a phase boundary separating the first- from the second-order transition. With the set of parameters used by R. Tiron et al. (2003) [25] and S. Hill et al. (2003) [20] to fit experimental data for [Mn4]2 dimer we find that the critical temperature at the phase boundary is T0(c)=0.29K. Therefore, thermally activated transitions should occur for temperatures greater than T0(c).

Accelerated molecular dynamics simulations of protein folding.

PubMed

Miao, Yinglong; Feixas, Ferran; Eun, Changsun; McCammon, J Andrew

2015-07-30

Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies. © 2015 Wiley Periodicals, Inc.

[Activities of Harvard College Observatory

NASA Technical Reports Server (NTRS)

Dalgarno, A.; Smith, Peter L.; Stark, G.; Yoshino, K.

2002-01-01

With support from this grant, we have: 1) Developed techniques for improving wavelengths and f-values for singly and doubly charged ions of the iron group and have improved the accuracy of Fe III wavelengths by an order of magnitude. New Fe II f-values have also resulted from this work. 2) Measured line oscillator strengths and photoabsorption cross sections for UV molecular spectral feature that have been, or could be, used for searches for and detection of molecules in diffuse and translucent interstellar clouds and for determination of molecular column densities there. In addition, we have determined other molecular parameters -- line assignments, wavelengths, and line widths -- that are essential for theoretical descriptions of the abundance, fractionation, and excitation of interstellar molecules and for comparison of predictions with observations. 3) Measured A-values for spin-changing and other weak lines in low-Z ions. When A-values are available, these spectral features are useful for astrophysical plasma density and temperature diagnostics. Such lines are also used in interstellar abundance determinations in cases where the stronger allowed lines are saturated in astronomical spectra. 4) Taken an activist approach to ensuring that, (i), astronomers have ready access to our data, and, (ii), avenues of communication between data users and producers are strengthened.

Transport properties of mixtures by the soft-SAFT + free-volume theory: application to mixtures of n-alkanes and hydrofluorocarbons.

PubMed

Llovell, F; Marcos, R M; Vega, L F

2013-05-02

In a previous paper (Llovell et al. J. Phys. Chem. B, submitted for publication), the free-volume theory (FVT) was coupled with the soft-SAFT equation of state for the first time to extend the capabilities of the equation to the calculation of transport properties. The equation was tested with molecular simulations and applied to the family of n-alkanes. The capability of the soft-SAFT + FVT treatment is extended here to other chemical families and mixtures. The compositional rules of Wilke (Wilke, C. R. J. Chem. Phys. 1950, 18, 517-519) are used for the diluted term of the viscosity, while the dense term is evaluated using very simple mixing rules to calculate the viscosity parameters. The theory is then used to predict the vapor-liquid equilibrium and the viscosity of mixtures of nonassociating and associating compounds. The approach is applied to determine the viscosity of a selected group of hydrofluorocarbons, in a similar manner as previously done for n-alkanes. The soft-SAFT molecular parameters are taken from a previous work, fitted to vapor-liquid equilibria experimental data. The application of FVT requires three additional parameters related to the viscosity of the pure fluid. Using a transferable approach, the α parameter is taken from the equivalent n-alkane, while the remaining two parameters B and Lv are fitted to viscosity data of the pure fluid at several isobars. The effect of these parameters is then investigated and compared to those obtained for n-alkanes, in order to better understand their effect on the calculations. Once the pure fluids are well characterized, the vapor-liquid equilibrium and the viscosity of nonassociating and associating mixtures, including n-alkane + n-alkane, hydrofluorocarbon + hydrofluorocarbon, and n-alkane + hydrofluorocarbon mixtures, are calculated. One or two binary parameters are used to account for deviations in the vapor-liquid equilibrium diagram for nonideal mixtures; these parameters are used in a transferable manner to predict the viscosity of the mixtures. Very good agreement with available experimental data is found in all cases, with an average absolute deviation ranging between 1.0% and 5.5%, even when the system presents azeotropy, reinforcing the robustness of the approach.

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

PubMed

Prior, Christopher; Oganesyan, Vasily S

2017-09-21

We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probes of turbulent driving mechanisms in molecular clouds from fluctuations in synchrotron intensity

NASA Astrophysics Data System (ADS)

Herron, C. A.; Federrath, C.; Gaensler, B. M.; Lewis, G. F.; McClure-Griffiths, N. M.; Burkhart, Blakesley

2017-04-01

Previous studies have shown that star formation depends on the driving of molecular cloud turbulence, and differences in the driving can produce an order of magnitude difference in the star formation rate. The turbulent driving is characterized by the parameter ζ, with ζ = 0 for compressive, curl-free driving (e.g. accretion or supernova explosions), and ζ = 1 for solenoidal, divergence-free driving (e.g. Galactic shear). Here we develop a new method to measure ζ from observations of synchrotron emission from molecular clouds. We calculate statistics of mock synchrotron intensity images produced from magnetohydrodynamic simulations of molecular clouds, in which the driving was controlled to produce different values of ζ. We find that the mean and standard deviation of the log-normalized synchrotron intensity are sensitive to ζ, for values of ζ between 0 (curl-free driving) and 0.5 (naturally mixed driving). We quantify the dependence of zeta on the direction of the magnetic field relative to the line of sight. We provide best-fitting formulae for ζ in terms of the log-normalized mean and standard deviation of synchrotron intensity, with which ζ can be determined for molecular clouds that have similar Alfvénic Mach number to our simulations. These formulae are independent of the sonic Mach number. Signal-to-noise ratios larger than 5, and angular resolutions smaller than 5 per cent of the cloud diameter, are required to apply these formulae. Although there are no firm detections of synchrotron emission from molecular clouds, by combining Green Bank Telescope and Very Large Array observations it should be possible to detect synchrotron emission from molecular clouds, thereby constraining the value of ζ.

Infrared spectrum, structural and optical properties and molecular docking study of 3-(4-fluorophenyl)-5-phenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde.

PubMed

Mary, Y Sheena; Panicker, C Yohannan; Sapnakumari, M; Narayana, B; Sarojini, B K; Al-Saadi, Abdulaziz A; Van Alsenoy, C; War, Javeed Ahmad; Fun, H K

2015-03-05

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 3-(4-fluorophenyl)-5-phenyl-4,5-dihydro-1H-pyrazole-1-carbaldehyde have been investigated experimentally and theoretically. The title compound was optimized using at HF and DFT levels of calculations. The B3LYP/6-311++G(d,p) (5D,7F) results and in agreement with experimental infrared bands. The normal modes are assigned using potential energy distribution. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using natural bonding orbital analysis. The frontier molecular orbital analysis is used to determine the charge transfer within the molecule. From molecular electrostatic potential map, it is evident that the negative electrostatic potential regions are mainly localized over the carbonyl group and mono substituted phenyl ring and are possible sites for electrophilic attack and, positive regions are localized around all para substituted phenyl and pyrazole ring, indicating possible sites for nucleophilic attack. First hyperpolarizability is calculated in order to find its role in nonlinear optics. The geometrical parameters are in agreement with experimental data. From the molecular docking studies, it is evident that the fluorine atom attached to phenyl ring and the carbonyl group attached to pyrazole ring are crucial for binding and the results draw us to the conclusion that the compound might exhibit phosphodiesterase inhibitory activity. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of non-equilibrium metal cooling on the interstellar medium

NASA Astrophysics Data System (ADS)

Capelo, Pedro R.; Bovino, Stefano; Lupi, Alessandro; Schleicher, Dominik R. G.; Grassi, Tommaso

2018-04-01

By using a novel interface between the modern smoothed particle hydrodynamics code GASOLINE2 and the chemistry package KROME, we follow the hydrodynamical and chemical evolution of an isolated galaxy. In order to assess the relevance of different physical parameters and prescriptions, we constructed a suite of 10 simulations, in which we vary the chemical network (primordial and metal species), how metal cooling is modelled (non-equilibrium versus equilibrium; optically thin versus thick approximation), the initial gas metallicity (from 10 to 100 per cent solar), and how molecular hydrogen forms on dust. This is the first work in which metal injection from supernovae, turbulent metal diffusion, and a metal network with non-equilibrium metal cooling are self-consistently included in a galaxy simulation. We find that properly modelling the chemical evolution of several metal species and the corresponding non-equilibrium metal cooling has important effects on the thermodynamics of the gas, the chemical abundances, and the appearance of the galaxy: the gas is typically warmer, has a larger molecular-gas mass fraction, and has a smoother disc. We also conclude that, at relatively high metallicity, the choice of molecular-hydrogen formation rates on dust is not crucial. Moreover, we confirm that a higher initial metallicity produces a colder gas and a larger fraction of molecular gas, with the low-metallicity simulation best matching the observed molecular Kennicutt-Schmidt relation. Finally, our simulations agree quite well with observations that link star formation rate to metal emission lines.

Testing the nature of reaction coordinate describing interaction of H2 with carbonyl carbon, activated by Lewis acid complexation, and the Lewis basic solvent: A Born-Oppenheimer molecular dynamics study with explicit solvent

NASA Astrophysics Data System (ADS)

Heshmat, Mojgan; Privalov, Timofei

2017-09-01

Using Born-Oppenheimer molecular dynamics (BOMD), we explore the nature of interactions between H2 and the activated carbonyl carbon, C(carbonyl), of the acetone-B(C6F5)3 adduct surrounded by an explicit solvent (1,4-dioxane). BOMD simulations at finite (non-zero) temperature with an explicit solvent produced long-lasting instances of significant vibrational perturbation of the H—H bond and H2-polarization at C(carbonyl). As far as the characteristics of H2 are concerned, the dynamical transient state approximates the transition-state of the heterolytic H2-cleavage. The culprit is the concerted interactions of H2 with C(carbonyl) and a number of Lewis basic solvent molecules—i.e., the concerted C(carbonyl)⋯H2⋯solvent interactions. On one hand, the results presented herein complement the mechanistic insight gained from our recent transition-state calculations, reported separately from this article. But on the other hand, we now indicate that an idea of the sufficiency of just one simple reaction coordinate in solution-phase reactions can be too simplistic and misleading. This article goes in the footsteps of the rapidly strengthening approach of investigating molecular interactions in large molecular systems via "computational experimentation" employing, primarily, ab initio molecular dynamics describing reactants-interaction without constraints of the preordained reaction coordinate and/or foreknowledge of the sampling order parameters.

Truncation effect on Taylor-Aris dispersion in lattice Boltzmann schemes: Accuracy towards stability

NASA Astrophysics Data System (ADS)

Ginzburg, Irina; Roux, Laetitia

2015-10-01

The Taylor dispersion in parabolic velocity field provides a well-known benchmark for advection-diffusion (ADE) schemes and serves as a first step towards accurate modeling of the high-order non-Gaussian effects in heterogeneous flow. While applying the Lattice Boltzmann ADE two-relaxation-times (TRT) scheme for a transport with given Péclet number (Pe) one should select six free-tunable parameters, namely, (i) molecular-diffusion-scale, equilibrium parameter; (ii) three families of equilibrium weights, assigned to the terms of mass, velocity and numerical-diffusion-correction, and (iii) two relaxation rates. We analytically and numerically investigate the respective roles of all these degrees of freedom in the accuracy and stability in the evolution of a Gaussian plume. For this purpose, the third- and fourth-order transient multi-dimensional analysis of the recurrence equations of the TRT ADE scheme is extended for a spatially-variable velocity field. The key point is in the coupling of the truncation and Taylor dispersion analysis which allows us to identify the second-order numerical correction δkT to Taylor dispersivity coefficient kT. The procedure is exemplified for a straight Poiseuille flow where δkT is given in a closed analytical form in equilibrium and relaxation parameter spaces. The predicted longitudinal dispersivity is in excellent agreement with the numerical experiments over a wide parameter range. In relatively small Pe-range, the relative dispersion error increases with Péclet number. This deficiency reduces in the intermediate and high Pe-range where it becomes Pe-independent and velocity-amplitude independent. Eliminating δkT by a proper parameter choice and employing specular reflection for zero flux condition on solid boundaries, the d2Q9 TRT ADE scheme may reproduce the Taylor-Aris result quasi-exactly, from very coarse to fine grids, and from very small to arbitrarily high Péclet numbers. Since free-tunable product of two eigenfunctions also controls stability of the model, the validity of the analytically established von Neumann stability diagram is examined in Poiseuille profile. The simplest coordinate-stencil subclass, which is the d2Q5 TRT bounce-back scheme, demonstrates the best performance and achieves the maximum accuracy for most stable relaxation parameters.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Uncertainty for calculating transport on Titan: A probabilistic description of bimolecular diffusion parameters

NASA Astrophysics Data System (ADS)

Plessis, S.; McDougall, D.; Mandt, K.; Greathouse, T.; Luspay-Kuti, A.

2015-11-01

Bimolecular diffusion coefficients are important parameters used by atmospheric models to calculate altitude profiles of minor constituents in an atmosphere. Unfortunately, laboratory measurements of these coefficients were never conducted at temperature conditions relevant to the atmosphere of Titan. Here we conduct a detailed uncertainty analysis of the bimolecular diffusion coefficient parameters as applied to Titan's upper atmosphere to provide a better understanding of the impact of uncertainty for this parameter on models. Because temperature and pressure conditions are much lower than the laboratory conditions in which bimolecular diffusion parameters were measured, we apply a Bayesian framework, a problem-agnostic framework, to determine parameter estimates and associated uncertainties. We solve the Bayesian calibration problem using the open-source QUESO library which also performs a propagation of uncertainties in the calibrated parameters to temperature and pressure conditions observed in Titan's upper atmosphere. Our results show that, after propagating uncertainty through the Massman model, the uncertainty in molecular diffusion is highly correlated to temperature and we observe no noticeable correlation with pressure. We propagate the calibrated molecular diffusion estimate and associated uncertainty to obtain an estimate with uncertainty due to bimolecular diffusion for the methane molar fraction as a function of altitude. Results show that the uncertainty in methane abundance due to molecular diffusion is in general small compared to eddy diffusion and the chemical kinetics description. However, methane abundance is most sensitive to uncertainty in molecular diffusion above 1200 km where the errors are nontrivial and could have important implications for scientific research based on diffusion models in this altitude range.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories.

PubMed

McGibbon, Robert T; Beauchamp, Kyle A; Harrigan, Matthew P; Klein, Christoph; Swails, Jason M; Hernández, Carlos X; Schwantes, Christian R; Wang, Lee-Ping; Lane, Thomas J; Pande, Vijay S

2015-10-20

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular orbital evaluation of charge flow dynamics in natural pigments based photosensitizers.

PubMed

Heera, Thekinneydath Rajan; Cindrella, Louis

2010-03-01

The relationship between structure and photo electrochemical property of ten natural pigments from plants, insects and microbes has been analyzed using density functional theory (DFT) at the B3LYP/6-31G(d) level. The essential parameters for their photoelectrochemical behaviour such as ground state geometries, electronic transition energies and oxidation potentials are computed. The attachment tendency of the anchoring groups, expressed as the deprotonation order, is determined by calculating the proton affinities at different sites of the molecules. A thorough analysis of the charge flow dynamics in the molecular orbitals (HOMO and LUMO) of these molecules has been carried out and presented to emphasize the role of these orbitals in effective charge separation, the important feature of photosensitizers for DSSC. This study highlights that the flexible spatial orientation provided by the bridging aliphatic unsaturation favours the oscillator strength and the hydroxyl anchor group attached to the ring of delocalized pi electron cloud acts as the effective anchor.

Influence of bottle storage time on colour, phenolic composition and sensory properties of sweet red wines.

PubMed

Marquez, Ana; Serratosa, Maria P; Merida, Julieta

2014-03-01

Changes in colour and phenolic composition in sweet red wines made from Merlot, Syrah and Tempranillo grapes were studied in order to assess the influence of bottle storage over a period of 12months. For this purpose, wine colour parameters, sensory analysis and concentrations of monomeric anthocyanins, pyranoanthocyanins, methylmethine-mediated condensation adducts, flavan3-ol derivatives and flavonols were measured. Hue increased and red colours decreased with the storage time, particularly over the first 3months. The concentrations of low molecular weight flavan-3-ol derivatives decreased with time due to the effect of their conversion into tannins of high molecular weight. In addition, the glycosylated flavonols decreased through hydrolysis to give the corresponding aglycones. Overall, the concentration of phenolic compounds decreased markedly with storage time, whereas the antioxidant activity in the wines remained constant throughout. A panel of expert tasters judged the colour, aroma and flavour of all initial and final wines to be acceptable. Copyright © 2013 Elsevier Ltd. All rights reserved.

Simulations of a Molecular Cloud experiment using CRASH

NASA Astrophysics Data System (ADS)

Trantham, Matthew; Keiter, Paul; Vandervort, Robert; Drake, R. Paul; Shvarts, Dov

2017-10-01

Recent laboratory experiments explore molecular cloud radiation hydrodynamics. The experiment irradiates a gold foil with a laser producing x-rays to drive the implosion or explosion of a foam ball. The CRASH code, an Eulerian code with block-adaptive mesh refinement, multigroup diffusive radiation transport, and electron heat conduction developed at the University of Michigan to design and analyze high-energy-density experiments, is used to perform a parameter search in order to identify optically thick, optically thin and transition regimes suitable for these experiments. Specific design issues addressed by the simulations are the x-ray drive temperature, foam density, distance from the x-ray source to the ball, as well as other complicating issues such as the positioning of the stalk holding the foam ball. We present the results of this study and show ways the simulations helped improve the quality of the experiment. This work is funded by the LLNL under subcontract B614207 and NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas, Grant Number DE-NA0002956.

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

PubMed Central

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernández, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.

2015-01-01

As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing MD simulations. MDTraj reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between MD data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. MDTraj is a powerful and user-friendly software package that simplifies the analysis of MD data and connects these datasets with the modern interactive data science software ecosystem in Python. PMID:26488642

A Theoretical Study on N'-[(Z)-(4-Methylphenyl)Methylidene]-4-Nitrobenzohydrazide (NMPMN)

NASA Astrophysics Data System (ADS)

Okur, Muhammet; Albayrak, Nazmiye; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

2018-05-01

Quantum mechanical calculations of ground state energy, vibration wavenumbers, and electronic absorption wavelengths of N'-[(Z)-(4-methylphenyl)methylidene]-4-nitrobenzohydrazide with C15H13N3O3 empirical formula was performed by using Gaussian 09 program. Becke's three-parameter exchange functional in conjunction with the Lee-Yang-Parr correlation functional and Heyd-Scuseria-Ernzerhof functional levels of density functional theory (DFT) with the 6-311++G(d,p) basis set were used in the performing of above mentioned calculations. The highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO) energies have been also calculated at the same levels. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) behavior of the title molecule has been examined by the determining of electric dipole moment (μ), polarizability (α), and static first-order hyperpolarizability (β). Finally, molecular electrostatic potential (MEP) surface as well as Mulliken and NBO atomic charges were calculated by using Gaussian 09 program.

Molecular dynamics simulation analysis of the effect of T790M mutation on epidermal growth factor receptor protein architecture in non-small cell lung carcinoma.

PubMed

Peng, Xiao-Nu; Wang, Jing; Zhang, Wei

2017-08-01

Non-small cell lung cancer etiology and its treatment failure are due to epidermal growth factor receptor (EGFR) kinase domain mutations at amino acid position 790. The mutational change from threonine to methionine at position 790 (T790M) is responsible for tyrosine kinase inhibition failure. Using molecular dynamic simulation, the present study investigated the architectural changes occurring at the atomic scale. The 50-nsec runs using a GROMOS force field for wild-type and mutant EGFR's kinase domains were investigated for contrasting variations using Gromacs inbuilt tools. The adenosine triphosphate binding domain and the active site of EGFR were studied extensively in order to understand the structural changes. All the parameters investigated in the present study revealed considerable changes in the studied structures, and the knowledge gained from this may be used to develop novel kinase inhibitors that will be effective irrespective of the structural alterations in kinase domain.

Molecular parameters involved in bee-plant relationships: a biological and chemical approach.

PubMed

Pham-Delegue, M H; Etievant, P; Masson, C

1987-01-01

Honeybee-plant relationships are based on a conditioning process in which olfactory (plant aroma) and gustatory cues (mainly nectars) are closely linked, leading to a selective foraging behaviour. Among crops dependent upon entomophilous cross-pollination, the sunflower has recently undergone extensive expansion due to hybrid variety selection. Sunflower hybrid seed production is strictly dependent upon pollinating insects, mainly the honeybees, but foragers may have preferences among the parental lines, leading to a lack of pollen carriage and consequently to a decrease of hybrid seed yield. In order to define the role of plant chemicals (aromas, nectars) involved in the pollination process, we set up a study combining behavioural and chemical assays. It appears that even though volatile chemical blends are much more complex compared to glucidic blends, for both kinds of cues only a 'limited chemical pattern' is responsible for foragers' choices. Therefore, it is henceforth possible to take these molecular criteria into account for plant improvement.

Structural analysis and antimicrobial activity of 2[1H]-pyrimidinethione/selenone derivatives

NASA Astrophysics Data System (ADS)

Żesławska, Ewa; Korona-Głowniak, Izabela; Szczesio, Małgorzata; Olczak, Andrzej; Żylewska, Alicja; Tejchman, Waldemar; Malm, Anna

2017-08-01

Four new crystal structures of sulfur and selenium analogues of 2[1H]-pyrimidinone derivatives were determined with the use of X-ray diffraction method. The molecular geometry and intermolecular interactions of the investigated molecules were analyzed in order to find the structural features and geometrical parameters, which can be responsible for antimicrobial activities. The influence of chalcogen substituents (sulfur and selenium) on the crystal packing was also studied. The main differences in the molecular structures exist in mutual arrangement of two aromatic rings. The intermolecular interactions in all investigated compounds are similar. Furthermore, the in vitro antibacterial and antifungal activities for these compounds were evaluated. Preliminary investigations have identified two highly potent antibacterial compounds containing selenium atom, which display selectivity towards staphylococci and micrococci. This selectivity was not observed for a control compound used as a drug, namely vancomycin. These compounds possess also good antifungal activity. This is the first report of biological activities of 2[1H]-pyrimidineselenone derivatives.

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

NASA Astrophysics Data System (ADS)

Choi, Jonathan W.; Li, Zhaodong; Black, Charles T.; Sweat, Daniel P.; Wang, Xudong; Gopalan, Padma

2016-06-01

In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01409g

Importance of dispersion and electron correlation in ab initio protein folding.

PubMed

He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

2009-04-16

Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

Effects of Atomic-Scale Structure on the Fracture Properties of Amorphous Carbon - Carbon Nanotube Composites

NASA Technical Reports Server (NTRS)

Jensen, Benjamin D.; Wise, Kristopher E.; Odegard, Gregory M.

2015-01-01

The fracture of carbon materials is a complex process, the understanding of which is critical to the development of next generation high performance materials. While quantum mechanical (QM) calculations are the most accurate way to model fracture, the fracture behavior of many carbon-based composite engineering materials, such as carbon nanotube (CNT) composites, is a multi-scale process that occurs on time and length scales beyond the practical limitations of QM methods. The Reax Force Field (ReaxFF) is capable of predicting mechanical properties involving strong deformation, bond breaking and bond formation in the classical molecular dynamics framework. This has been achieved by adding to the potential energy function a bond-order term that varies continuously with distance. The use of an empirical bond order potential, such as ReaxFF, enables the simulation of failure in molecular systems that are several orders of magnitude larger than would be possible in QM techniques. In this work, the fracture behavior of an amorphous carbon (AC) matrix reinforced with CNTs was modeled using molecular dynamics with the ReaxFF reactive forcefield. Care was taken to select the appropriate simulation parameters, which can be different from those required when using traditional fixed-bond force fields. The effect of CNT arrangement was investigated with three systems: a single-wall nanotube (SWNT) array, a multi-wall nanotube (MWNT) array, and a SWNT bundle system. For each arrangement, covalent bonds are added between the CNTs and AC, with crosslink fractions ranging from 0-25% of the interfacial CNT atoms. The SWNT and MWNT array systems represent ideal cases with evenly spaced CNTs; the SWNT bundle system represents a more realistic case because, in practice, van der Waals interactions lead to the agglomeration of CNTs into bundles. The simulation results will serve as guidance in setting experimental processing conditions to optimize the mechanical properties of CNT composites.

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

PubMed

Paliwal, Himanshu; Shirts, Michael R

2013-11-12

Multistate reweighting methods such as the multistate Bennett acceptance ratio (MBAR) can predict free energies and expectation values of thermodynamic observables at poorly sampled or unsampled thermodynamic states using simulations performed at only a few sampled states combined with single point energy reevaluations of these samples at the unsampled states. In this study, we demonstrate the power of this general reweighting formalism by exploring the effect of simulation parameters controlling Coulomb and Lennard-Jones cutoffs on free energy calculations and other observables. Using multistate reweighting, we can quickly identify, with very high sensitivity, the computationally least expensive nonbonded parameters required to obtain a specified accuracy in observables compared to the answer obtained using an expensive "gold standard" set of parameters. We specifically examine free energy estimates of three molecular transformations in a benchmark molecular set as well as the enthalpy of vaporization of TIP3P. The results demonstrates the power of this multistate reweighting approach for measuring changes in free energy differences or other estimators with respect to simulation or model parameters with very high precision and/or very low computational effort. The results also help to identify which simulation parameters affect free energy calculations and provide guidance to determine which simulation parameters are both appropriate and computationally efficient in general.

Microscopic cascading of second-order molecular nonlinearity: New design principles for enhancing third-order nonlinearity.

PubMed

Baev, Alexander; Autschbach, Jochen; Boyd, Robert W; Prasad, Paras N

2010-04-12

Herein, we develop a phenomenological model for microscopic cascading and substantiate it with ab initio calculations. It is shown that the concept of local microscopic cascading of a second-order nonlinearity can lead to a third-order nonlinearity, without introducing any new loss mechanisms that could limit the usefulness of our approach. This approach provides a new molecular design protocol, in which the current great successes achieved in producing molecules with extremely large second-order nonlinearity can be used in a supra molecular organization in a preferred orientation to generate very large third-order response magnitudes. The results of density functional calculations for a well-known second-order molecule, (para)nitroaniline, show that a head-to-tail dimer configuration exhibits enhanced third-order nonlinearity, in agreement with the phenomenological model which suggests that such an arrangement will produce cascading due to local field effects.

Degradation of polycyclic aromatic hydrocarbons (PAHs) in textile dyeing sludge with ultrasound and Fenton processes: Effect of system parameters and synergistic effect study.

PubMed

Lin, Meiqing; Ning, Xun-an; An, Taicheng; Zhang, Jianhao; Chen, Changmin; Ke, Yaowei; Wang, Yujie; Zhang, Yaping; Sun, Jian; Liu, Jingyong

2016-04-15

To establish an efficient oxidation process for the degradation of polycyclic aromatic hydrocarbons (PAHs) in textile dyeing sludge, the effects of various operating parameters were optimized during the ultrasound process, Fenton process and the combined ultrasound-Fenton process. The results showed that the ultrasonic density of 1.80w/cm(3), both H2O2 and Fe(2+) dosages of 140mmol/L and pH 3 were favorable conditions for the degradation of PAHs. The degradation efficiency of high molecular weight PAHs was close to or even higher than that of light molecular weight PAHs. The highest degradation efficiencies of Σ16 PAHs were obtained within 30min in the order of: Fenton (83.5%) >ultrasound-Fenton (75.5%) >ultrasound (45.5%), then the efficiencies were decreased in the other of: ultrasound-Fenton (73.0%) >Fenton (70.3%) >ultrasound (41.4%) in 60min. The extra PAHs were released from the intracellular substances and the cavities of sludge due to the disruption of sludge during the oxidation process. Also, the degradation of PAHs could be inhibited by the other organic matter in the sludge. The combined ultrasound-Fenton process showed more efficient than both ultrasound process and Fenton process not only in the surface of sludge but also in the sludge interior. Copyright © 2015 Elsevier B.V. All rights reserved.

First principles crystal engineering of nonlinear optical materials. I. Prototypical case of urea

NASA Astrophysics Data System (ADS)

Masunov, Artëm E.; Tannu, Arman; Dyakov, Alexander A.; Matveeva, Anastasia D.; Freidzon, Alexandra Ya.; Odinokov, Alexey V.; Bagaturyants, Alexander A.

2017-06-01

The crystalline materials with nonlinear optical (NLO) properties are critically important for several technological applications, including nanophotonic and second harmonic generation devices. Urea is often considered to be a standard NLO material, due to the combination of non-centrosymmetric crystal packing and capacity for intramolecular charge transfer. Various approaches to crystal engineering of non-centrosymmetric molecular materials were reported in the literature. Here we propose using global lattice energy minimization to predict the crystal packing from the first principles. We developed a methodology that includes the following: (1) parameter derivation for polarizable force field AMOEBA; (2) local minimizations of crystal structures with these parameters, combined with the evolutionary algorithm for a global minimum search, implemented in program USPEX; (3) filtering out duplicate polymorphs produced; (4) reoptimization and final ranking based on density functional theory (DFT) with many-body dispersion (MBD) correction; and (5) prediction of the second-order susceptibility tensor by finite field approach. This methodology was applied to predict virtual urea polymorphs. After filtering based on packing similarity, only two distinct packing modes were predicted: one experimental and one hypothetical. DFT + MBD ranking established non-centrosymmetric crystal packing as the global minimum, in agreement with the experiment. Finite field approach was used to predict nonlinear susceptibility, and H-bonding was found to account for a 2.5-fold increase in molecular hyperpolarizability to the bulk value.

Hydration effects on the electrostatic potential around tuftsin.

PubMed

Valdeavella, C V; Blatt, H D; Yang, L; Pettitt, B M

1999-08-01

The electrostatic potential and component dielectric constants from molecular dynamics (MD) trajectories of tuftsin, a tetrapeptide with the amino acid sequence Thr-Lys-Pro-Arg in water and in saline solution are presented. The results obtained from the analysis of the MD trajectories for the total electrostatic potential at points on a grid using the Ewald technique are compared with the solution to the Poisson-Boltzmann (PB) equation. The latter was solved using several sets of dielectric constant parameters. The effects of structural averaging on the PB results were also considered. Solute conformational mobility in simulations gives rise to an electrostatic potential map around the solute dominated by the solute monopole (or lowest order multipole). The detailed spatial variation of the electrostatic potential on the molecular surface brought about by the compounded effects of the distribution of water and ions close to the peptide, solvent mobility, and solute conformational mobility are not qualitatively reproducible from a reparametrization of the input solute and solvent dielectric constants to the PB equation for a single structure or for structurally averaged PB calculations. Nevertheless, by fitting the PB to the MD electrostatic potential surfaces with the dielectric constants as fitting parameters, we found that the values that give the best fit are the values calculated from the MD trajectories. Implications of using such field calculations on the design of tuftsin peptide analogues are discussed.

Synthesis, characterization, and binding assessment with human serum albumin of three bipyridine lanthanide(III) complexes.

PubMed

Aramesh-Boroujeni, Zahra; Bordbar, Abdol-Khalegh; Khorasani-Motlagh, Mozhgan; Sattarinezhad, Elham; Fani, Najme; Noroozifar, Meissam

2018-05-18

In this work, the terbium(III), dysprosium(III), and ytterbium(III) complexes containing 2, 2'-bipyridine (bpy) ligand have been synthesized and characterized using CHN elemental analysis, FT-IR, UV-Vis and 1 H-NMR techniques and their binding behavior with human serum albumin (HSA) was studied by UV-Vis, fluorescence and molecular docking examinations. The experimental data indicated that all three lanthanide complexes have high binding affinity to HSA with effective quenching of HSA fluorescence via static mechanism. The binding parameters, the type of interaction, the value of resonance energy transfer, and the binding distance between complexes and HSA were estimated from the analysis of fluorescence measurements and Förster theory. The thermodynamic parameters suggested that van der Waals interactions and hydrogen bonds play an important role in the binding mechanism. While, the energy transfer from HSA molecules to all these complexes occurs with high probability, the order of binding constants (BpyTb > BpyDy > BpyYb) represents the importance of radius of Ln 3+ ion in the complex-HSA interaction. The results of molecular docking calculation and competitive experiments assessed site 3 of HSA, located in subdomain IB, as the most probable binding site for these ligands and also indicated the microenvironment residues around the bound mentioned complexes. The computational results kept in good agreement with experimental data.

Fine Tuning of Tissues' Viscosity and Surface Tension through Contractility Suggests a New Role for α-Catenin

PubMed Central

Stirbat, Tomita Vasilica; Mgharbel, Abbas; Bodennec, Selena; Ferri, Karine; Mertani, Hichem C.; Rieu, Jean-Paul; Delanoë-Ayari, Hélène

2013-01-01

What governs tissue organization and movement? If molecular and genetic approaches are able to give some answers on these issues, more and more works are now giving a real importance to mechanics as a key component eventually triggering further signaling events. We chose embryonic cell aggregates as model systems for tissue organization and movement in order to investigate the origin of some mechanical constraints arising from cells organization. Steinberg et al. proposed a long time ago an analogy between liquids and tissues and showed that indeed tissues possess a measurable tissue surface tension and viscosity. We question here the molecular origin of these parameters and give a quantitative measurement of adhesion versus contractility in the framework of the differential interfacial tension hypothesis. Accompanying surface tension measurements by angle measurements (at vertexes of cell-cell contacts) at the cell/medium interface, we are able to extract the full parameters of this model: cortical tensions and adhesion energy. We show that a tunable surface tension and viscosity can be achieved easily through the control of cell-cell contractility compared to cell-medium one. Moreover we show that -catenin is crucial for this regulation to occur: these molecules appear as a catalyser for the remodeling of the actin cytoskeleton underneath cell-cell contact, enabling a differential contractility between the cell-medium and cell-cell interface to take place. PMID:23390488

Mapping MRI/MRS Parameters with Genetic Over-expression Profiles In Human Prostate Cancer: Demonstrating the Potential

PubMed Central

Lenkinski, Robert E.; Bloch, B. Nicholas; Liu, Fangbing; Frangioni, John V.; Perner, Sven; Rubin, Mark A.; Genega, Elizabeth; Rofsky, Neil M.; Gaston, Sandra M.

2009-01-01

Magnetic resonance imaging (MRI) and MR spectroscopy can probe a variety of physiological (e.g. blood vessel permeability) and metabolic characteristics of prostate cancer. However, little is known about the changes in gene expression that underlie the spectral and imaging features observed in prostate cancer. Tumor induced changes in vascular permeability and angiogenesis are thought to contribute to patterns of dynamic contrast enhanced (DCE) MRI images of prostate cancer even though the genetic basis of tumor vasculogenesis is complex and the specific mechanisms underlying these DCEMRI features have not yet been determined. In order to identify the changes in gene expression that correspond to MRS and DCEMRI patterns in human prostate cancers, we have utilized tissue print micropeel techniques to generate “whole mount” molecular maps of radical prostatectomy specimens that correspond to pre-surgical MRI/MRS studies. These molecular maps include RNA expression profiles from both Affymetrix GeneChip microarrays and quantitative reverse transcriptase PCR (qrt-PCR) analysis, as well as immunohistochemical studies. Using these methods on patients with prostate cancer, we found robust over-expression of choline kinase a in the majority of primary tumors. We also observed overexpression of neuropeptide Y (NPY), a newly identified angiogenic factor, in a subset of DCEMRI positive prostate cancers. These studies set the stage for establishing MRI/MRS parameters as validated biomarkers for human prostate cancer. PMID:18752015

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

PubMed

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

A Quantitative Structure-Property Relationship (QSPR) Study of Aliphatic Alcohols by the Method of Dividing the Molecular Structure into Substructure

PubMed Central

Liu, Fengping; Cao, Chenzhong; Cheng, Bin

2011-01-01

A quantitative structure–property relationship (QSPR) analysis of aliphatic alcohols is presented. Four physicochemical properties were studied: boiling point (BP), n-octanol–water partition coefficient (lg POW), water solubility (lg W) and the chromatographic retention indices (RI) on different polar stationary phases. In order to investigate the quantitative structure–property relationship of aliphatic alcohols, the molecular structure ROH is divided into two parts, R and OH to generate structural parameter. It was proposed that the property is affected by three main factors for aliphatic alcohols, alkyl group R, substituted group OH, and interaction between R and OH. On the basis of the polarizability effect index (PEI), previously developed by Cao, the novel molecular polarizability effect index (MPEI) combined with odd-even index (OEI), the sum eigenvalues of bond-connecting matrix (SX1CH) previously developed in our team, were used to predict the property of aliphatic alcohols. The sets of molecular descriptors were derived directly from the structure of the compounds based on graph theory. QSPR models were generated using only calculated descriptors and multiple linear regression techniques. These QSPR models showed high values of multiple correlation coefficient (R > 0.99) and Fisher-ratio statistics. The leave-one-out cross-validation demonstrated the final models to be statistically significant and reliable. PMID:21731451

Molecular docking, spectroscopic studies and quantum calculations on nootropic drug.

PubMed

Uma Maheswari, J; Muthu, S; Sundius, Tom

2014-04-05

A systematic vibrational spectroscopic assignment and analysis of piracetam [(2-oxo-1-pyrrolidineacetamide)] have been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G++(d,p) basis set. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, and harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption wavelengths λmax were determined by the time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PED) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. Molecular docking studies have been carried out in the active site of piracetam by using Argus Lab. In addition, the potential energy surface, HOMO and LUMO energies, first-order hyperpolarizability and the molecular electrostatic potential have been computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Experimental Raman and IR spectral and theoretical studies of vibrational spectrum and molecular structure of Pantothenic acid (vitamin B5)

NASA Astrophysics Data System (ADS)

Srivastava, Mayuri; Singh, N. P.; Yadav, R. A.

2014-08-01

Vibrational spectrum of Pantothenic acid has been investigated using experimental IR and Raman spectroscopies and density functional theory methods available with the Gaussian 09 software. Vibrational assignments of the observed IR and Raman bands have been proposed in light of the results obtained from computations. In order to assign the observed IR and Raman frequencies the potential energy distributions (PEDs) have also been computed using GAR2PED software. Optimized geometrical parameters suggest that the overall symmetry of the molecule is C1. The molecule is found to possess eight conformations. Conformational analysis was carried out to obtain the most stable configuration of the molecule. In the present paper the vibrational features of the lowest energy conformer C-I have been studied. The two methyl groups have slightly distorted symmetries from C3V. The acidic Osbnd H bond is found to be the smallest one. To investigate molecular stability and bond strength we have used natural bond orbital analysis (NBO). Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energies. The mapping of electron density iso-surface with electrostatic potential (ESP), has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule.

Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA.

PubMed

Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

2018-03-15

Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 10 3 M -1 , which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) were -63.19kJ mol -1 and -141.92J mol -1 K -1 , indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of chain stiffness on the competition between crystallization and glass-formation in model unentangled polymers

NASA Astrophysics Data System (ADS)

Nguyen, Hong T.; Smith, Tyler B.; Hoy, Robert S.; Karayiannis, Nikos Ch.

2015-10-01

We map out the solid-state morphologies formed by model soft-pearl-necklace polymers as a function of chain stiffness, spanning the range from fully flexible to rodlike chains. The ratio of Kuhn length to bead diameter (lK/r0) increases monotonically with increasing bending stiffness kb and yields a one-parameter model that relates chain shape to bulk morphology. In the flexible limit, monomers occupy the sites of close-packed crystallites while chains retain random-walk-like order. In the rodlike limit, nematic chain ordering typical of lamellar precursors coexists with close-packing. At intermediate values of bending stiffness, the competition between random-walk-like and nematic chain ordering produces glass-formation; the range of kb over which this occurs increases with the thermal cooling rate | T ˙ | implemented in our molecular dynamics simulations. Finally, values of kb between the glass-forming and rodlike ranges produce complex ordered phases such as close-packed spirals. Our results should provide a useful initial step in a coarse-grained modeling approach to systematically determining the effect of chain stiffness on the crystallization-vs-glass-formation competition in both synthetic and colloidal polymers.

Orientational ordering of lamellar structures on closed surfaces

NASA Astrophysics Data System (ADS)

PÈ©kalski, J.; Ciach, A.

2018-05-01

Self-assembly of particles with short-range attraction and long-range repulsion interactions on a flat and on a spherical surface is compared. Molecular dynamics simulations are performed for the two systems having the same area and the density optimal for formation of stripes of particles. Structural characteristics, e.g., a cluster size distribution, a number of defects, and an orientational order parameter (OP), as well as the specific heat, are obtained for a range of temperatures. In both cases, the cluster size distribution becomes bimodal and elongated clusters appear at the temperature corresponding to the maximum of the specific heat. When the temperature decreases, orientational ordering of the stripes takes place and the number of particles per cluster or stripe increases in both cases. However, only on the flat surface, the specific heat has another maximum at the temperature corresponding to a rapid change of the OP. On the sphere, the crossover between the isotropic and anisotropic structures occur in a much broader temperature interval; the orientational order is weaker and occurs at significantly lower temperature. At low temperature, the stripes on the sphere form spirals and the defects resemble defects in the nematic phase of rods adsorbed at a sphere.

Simple and Reliable Method to Quantify the Hepatitis B Viral Load and Replicative Capacity in Liver Tissue and Blood Leukocytes

PubMed Central

Minosse, Claudia; Coen, Sabrina; Visco Comandini, Ubaldo; Lionetti, Raffaella; Montalbano, Marzia; Cerilli, Stefano; Vincenti, Donatella; Baiocchini, Andrea; Capobianchi, Maria R.; Menzo, Stefano

2016-01-01

Background A functional cure of chronic hepatitis B (CHB) is feasible, but a clear view of the intrahepatic viral dynamics in each patient is needed. Intrahepatic covalently closed circular DNA (cccDNA) is the stable form of the viral genome in infected cells, and represents the ideal marker of parenchymal colonization. Its relationships with easily accessible peripheral parameters need to be elucidated in order to avoid invasive procedures in patients. Objectives The goal of this study was to design, set up, and validate a reliable and straightforward method for the quantification of the cccDNA and total DNA of the hepatitis B virus (HBV) in a variety of clinical samples. Patients and Methods Clinical samples from a cohort of CHB patients, including liver biopsies in some, were collected for the analysis of intracellular HBV molecular markers using novel molecular assays. Results A plasmid construct, including sequences from the HBV genome and from the human gene hTERT, was generated as an isomolar multi-standard for HBV quantitation and normalization to the cellular contents. The specificity of the real-time assay for the cccDNA was assessed using Dane particles isolated on a density gradient. A comparison of liver tissue from 6 untreated and 6 treated patients showed that the treatment deeply reduced the replicative capacity (total DNA/cccDNA), but had limited impact on the parenchymal colonization. The peripheral blood mononuclear cells (PBMCs) and granulocytes from the treated and untreated patients were also analyzed. Conclusions A straightforward method for the quantification of intracellular HBV molecular parameters in clinical samples was developed and validated. The widespread use of such versatile assays could better define the prognosis of CHB, and allow a more rational approach to time-limited tailored treatment strategies. PMID:27882060

Hemoglobin binding of aromatic amines: molecular dosimetry and quantitative structure-activity relationships for N-oxidation.

PubMed Central

Sabbioni, G

1993-01-01

Aromatic amines are important intermediates in industrial manufacturing. N-Oxidation to N-hydroxyarylamines is a key step in determining the genotoxic properties of aromatic amines. N-Hydroxyarylamines can form adducts with DNA, with tissue proteins, and with the blood proteins albumin and hemoglobin in a dose-dependent manner. The determination of hemoglobin adducts is a useful tool for biomonitoring exposed populations. We have established the hemoglobin binding index (HBI) [(mmole compound/mole hemoglobin)/(mmole compound/kg body weight)] of several aromatic amines in female Wistar rats. Including the values from other researchers obtained in the same rat strain, the logarithm of hemoglobin binding (logHBI) was plotted against the following parameters: the sum of the Hammett constants(sigma sigma = sigma p + sigma m), pKa, logP (octanol/water), the half-wave oxidation potential (E1/2), and the electronic descriptors of the amines and their corresponding nitrenium ions obtained by semi-empirical calculations (MNDO, AMI, and PM3), such as atomic charge densities, energies of the highest occupied molecular orbit and lowest occupied molecular orbit and their coefficients, the bond order of C-N, the dipole moments, and the reaction enthalpy [MNDOHF, AM1HF or PM3HF = Hf(nitrenium) - Hf(amine)]. The correlation coefficients were determined from the plots of all parameters against log HBI for all amines by means of linear regression analysis. The amines were classified in three groups: group 1, all parasubstituted amines (maximum, n = 9); group 2, all amines with halogens (maximun, n = 11); and group 3, all amines with alkyl groups (maximum, n = 13).(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8319626