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

Development and Assessment of a Molecular Structure and Properties Learning Progression

ERIC Educational Resources Information Center

Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.; Klymkowsky, Michael W.

2012-01-01

Previously, we found that: (i) many students were unable to construct representations of simple molecular structures; (ii) a majority of students fail to make the important connection between these representations and macroscopic properties of the material; and (iii) they were unable to decode the information contained in such representations.…

Looking beyond Lewis Structures: A General Chemistry Molecular Modeling Experiment Focusing on Physical Properties and Geometry

ERIC Educational Resources Information Center

Linenberger, Kimberly J.; Cole, Renee S.; Sarkar, Somnath

2011-01-01

We present a guided-inquiry experiment using Spartan Student Version, ready to be adapted and implemented into a general chemistry laboratory course. The experiment provides students an experience with Spartan Molecular Modeling software while discovering the relationships between the structure and properties of molecules. Topics discussed within…

[Strategy of molecular design of drugs: the unification of macro-properties and micro-structures of a molecule].

PubMed

Guo, Zong-Ru

2008-03-01

The interaction of a drug with the organism involves both the disposition of a drug by the organism and the action of a drug on the organism. The disposition of various exogenous substances, including drugs, complies with general rules. The underlying physical and chemical changes to different drugs in view of time and space, i. e. pharmacokinetics, share common characteristics, that is the tout ensemble of a molecule and its macroscopic properties convey direct effect on the pharmacokinetic behavior as the tendency and consequence of biological evolution. The action of a drug on the organism, on the other hand, implicates the physico-chemical binding of a drug molecule to the target protein, which induces pharmacological and toxicological effects. The biological reactions, no matter beneficial or adverse, are all specific and individual manifestation of the drug molecule and determined by the interactive binding between definitive atoms or groups of the drug molecule and the macromolecular target in three-dimension. Such critical atoms, groups, or fragments responsible for the interaction reflect the microscopic structures of drug molecules and are called pharmacophore. In this context, a drug molecule is presumed as an assembly of macroscopic property and microscopic structure, with the macroscopic properties determining the absorption, distribution, metabolism and elimination of drugs and the microscopic structure coining pharmacological action. The knowledge of the internal relationship between macroscopy/microscopy and PK/PD conduces to comprehension of drug action and guides molecular drug design, because this conception facilitates the identification of structural features necessary for biological response, and the determination of factors modulating the physico-chemical and pharmacokinetic properties. The factors determining macro-properties include molecular weight, solubility, charge, lipophilicity (partition), and polar surface area, etc., which are destined by molecular scaffolds and/or side chain(s) apart from pharmacophore. The features of micro-structures contributing to specific activity contain hydrogen bonding donor and acceptor, positive and negative charge centers, hydrophobic centers and centers of aromatic rings. Different combinations and spacial arrangements of these features determine the distinct activity presented. The macro-property and micro-structure are integrated into a single molecule, and are inseparable. The macro-property reflects overall contribution of atoms and groups in the micro-structure. On the other hand, structural changes aimed to adjust macroscopic property usually alter the relative position of the microscopic structure. The goal of molecular drug design is to integrate the macroscopic and microscopic factors in optimized manner. In the early stage of molecular design, both macroscopic property and microscopic structure should be considered to make pharmacodynamics, pharmacokinetics, and physico-chemical properties in optimal match. Therefore, it required the existence of structural overlapping among acceptable pharmacokinetics, visible developing potential and specific pharmacodynamics. The larger the scope of overlapping, the higher the possibility to be a drug.

Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

PubMed

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

An Investigation of College Chemistry Students' Understanding of Structure-Property Relationships

ERIC Educational Resources Information Center

Cooper, Melanie M.; Corley, Leah M.; Underwood, Sonia M.

2013-01-01

The connection between the molecular-level structure of a substance and its macroscopic properties is a fundamental concept in chemistry. Students in college-level general and organic chemistry courses were interviewed to investigate how they used structure-property relationships to predict properties such as melting and boiling points. Although…

Rationalizing the photophysical properties of BODIPY laser dyes via aromaticity and electron-donor-based structural perturbations

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

Waddell, Paul G.; Liu, Xiaogang; Zhao, Teng

2015-05-01

The absorption and fluorescence properties of six boron dipyrromethene (BODIPY) laser dyes with simple non-aromatic substituents are rationalized by relating them to observable structural perturbations within the molecules of the dyes. An empirical relationship involving the structure and the optical properties is derived using a combination of single-crystal X-ray diffraction data, quantum chemical calculations and electronic constants: i.e. the tendency of the pyrrole bond lengths towards aromaticity and the UV-vis absorption and fluorescence wavelengths correlating with the electron-donor properties of the substituents. The effect of molecular conformation on the solid-state optical properties of the dyes is also discussed. The findingsmore » in this study also demonstrate the usefulness and limitations of using crystal structure data to develop structure-property relationships in this class of optical materials, contributing to the growing effort to design optoelectronic materials with tunable properties via molecular engineering.« less

Development and Validation of the Implicit Information from Lewis Structures Instrument(IILSI): Do Students Connect Structures with Properties?

ERIC Educational Resources Information Center

Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.

2012-01-01

Lewis structures are a simplified two dimensional "cartoon" of molecular structure that allow a knowledgeable user to predict the types of properties a particular substance may exhibit. However, prior research shows that many students fail to recognize these structure-property connections and are unable to decode the information…

Chemodiversity and molecular plasticity: recognition processes as explored by property spaces.

PubMed

Vistoli, Giulio; Pedretti, Alessandro; Testa, Bernard

2011-06-01

In the last few years, a need to account for molecular flexibility in drug-design methodologies has emerged, even if the dynamic behavior of molecular properties is seldom made explicit. For a flexible molecule, it is indeed possible to compute different values for a given conformation-dependent property and the ensemble of such values defines a property space that can be used to describe its molecular variability; a most representative case is the lipophilicity space. In this review, a number of applications of lipophilicity space and other property spaces are presented, showing that this concept can be fruitfully exploited: to investigate the constraints exerted by media of different levels of structural organization, to examine processes of molecular recognition and binding at an atomic level, to derive informative descriptors to be included in quantitative structure--activity relationships and to analyze protein simulations extracting the relevant information. Much molecular information is neglected in the descriptors used by medicinal chemists, while the concept of property space can fill this gap by accounting for the often-disregarded dynamic behavior of both small ligands and biomacromolecules. Property space also introduces some innovative concepts such as molecular sensitivity and plasticity, which appear best suited to explore the ability of a molecule to adapt itself to the environment variously modulating its property and conformational profiles. Globally, such concepts can enhance our understanding of biological phenomena providing fruitful descriptors in drug-design and pharmaceutical sciences.

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations

PubMed Central

Yoo, Jejoong; Aksimentiev, Aleksei

2013-01-01

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840

In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

PubMed

Yoo, Jejoong; Aksimentiev, Aleksei

2013-12-10

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

Molecular structure of sodium lignosulfonate from different sources and their properties as dispersant of TiO2 slurry

Treesearch

Haifeng Zhou; Dongjie Yang; Junyong Zhu

2016-01-01

The molecular structure and properties of four sodium lignosulfates (LSs) derived from pulping or bioethanol production were evaluated and compared. SXP and SAL were produced by sulfite pulping and sulfonation reaction of lignin from alkali pulping of poplar, respectively. LS-180 and LS-150 were from sulfite pretreatment to overcome recalcitrance of lignocelluloses (...

Correlation of physical properties with molecular structure for some dicyclic hydrocarbons having high thermal-energy release per unit volume

NASA Technical Reports Server (NTRS)

Wise, P H; Serijan, K T; Goodman, I A

1951-01-01

As part of a program to study the correlation between molecular structure and physical properties of high-density hydrocarbons, the net heats of combustion, melting points, boiling points, densities, and kinematic viscosities of some hydrocarbons in the 2-n-alkylbiphenyl, 1,1-diphenylalkane, diphenylalkane, 1,1-dicyclohexylalkane, and dicyclohexylalkane series are presented.

New Synthesis Of Poly(1,3,4-Oxadiazoles)

NASA Technical Reports Server (NTRS)

Connell, John W.; Hergenrother, Paul M.; Wolf, Peter

1992-01-01

Synthesis via aromatic nucleophilic displacement yields new high-molecular-weight polymers. Polymers exhibited good mechanical and thermal properties. Synthetic route provided high-molecular-weight POX of new chemical structure, potentially more economical. Availability of large variety of activated aromatic dihalides, facilitates variation of chemical structures. Exhibit properties making them useful as films. Also useful in coatings, adhesives, moldings, and composites.

Structures and spectroscopic properties of nonperipherally and peripherally substituted metal-free phthalocyanines: a substitution effect study based on density functional theory calculations.

PubMed

Zhong, Aimin; Zhang, Yuexing; Bian, Yongzhong

2010-11-01

The molecular structures, molecular orbitals, atomic charges, electronic absorption spectra, and infrared (IR) and Raman spectra of a series of substituted metal-free phthalocyanine compounds with four (1, 3, 5, 7) or eight (2, 4, 6, 8) methoxyl (1, 2, 5, 6) or methylthio groups (3, 4, 7, 8) on the nonperipheral (1-4) or peripheral positions (5-8) of the phthalocyanine ring are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The calculated structural parameters and simulated electronic absorption and IR spectra are compared with the X-ray crystallography structures and the experimentally observed electronic absorption and IR spectra of the similar molecules, and good agreement between the calculated and experimental results is found. The substitution of the methoxyl or methylthio groups at the nonperipheral positions of the phthalocyanine ring has obvious effects on the molecular structure and spectroscopic properties of the metal-free phthalocyanine. Nonperipheral substitution has a more significant influence than peripheral substitution. The substitution effect increases with an increase in the number of substituents. The methylthio group shows more significant influence than the methoxyl group, despite the stronger electron-donating property of the methoxyl group than the methylthio group. The octa-methylthio-substituted metal-free phthalocyanine compounds have nonplanar structures whose low-lying occupied molecular orbitals and electronic absorption spectra are significantly changed by the substituents. The present systematical study will be helpful for understanding the relationship between structures and properties in phthalocyanine compounds and designing phthalocyanines with typical properties. Copyright © 2010 Elsevier Inc. All rights reserved.

Modeling the chemistry of complex petroleum mixtures.

PubMed Central

Quann, R J

1998-01-01

Determining the complete molecular composition of petroleum and its refined products is not feasible with current analytical techniques because of the astronomical number of molecular components. Modeling the composition and behavior of such complex mixtures in refinery processes has accordingly evolved along a simplifying concept called lumping. Lumping reduces the complexity of the problem to a manageable form by grouping the entire set of molecular components into a handful of lumps. This traditional approach does not have a molecular basis and therefore excludes important aspects of process chemistry and molecular property fundamentals from the model's formulation. A new approach called structure-oriented lumping has been developed to model the composition and chemistry of complex mixtures at a molecular level. The central concept is to represent an individual molecular or a set of closely related isomers as a mathematical construct of certain specific and repeating structural groups. A complex mixture such as petroleum can then be represented as thousands of distinct molecular components, each having a mathematical identity. This enables the automated construction of large complex reaction networks with tens of thousands of specific reactions for simulating the chemistry of complex mixtures. Further, the method provides a convenient framework for incorporating molecular physical property correlations, existing group contribution methods, molecular thermodynamic properties, and the structure--activity relationships of chemical kinetics in the development of models. PMID:9860903

Skin hydration: interplay between molecular dynamics, structure and water uptake in the stratum corneum.

PubMed

Mojumdar, Enamul Haque; Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

2017-11-16

Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca. 85% relative humidity (RH). The abrupt changes in SC molecular properties coincide with changes in SC macroscopic swelling properties as well as mechanical properties in the SC. The flexible terminals at the solid keratin filaments can be compared to flexible polymer brushes in colloidal systems, creating long-range repulsion and extensive swelling in water. We further show that the addition of urea to the SC at reduced RH leads to similar molecular and macroscopic responses as the increase in RH for SC without urea. The findings provide new molecular insights to deepen the understanding of how intermediate filament organization responds to changes in the surrounding environment.

Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins

NASA Astrophysics Data System (ADS)

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-01

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm- 1 and 1545 cm- 1, respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties.

Synthesis of one-dimensional metal-containing insulated molecular wire with versatile properties directed toward molecular electronics materials.

PubMed

Masai, Hiroshi; Terao, Jun; Seki, Shu; Nakashima, Shigeto; Kiguchi, Manabu; Okoshi, Kento; Fujihara, Tetsuaki; Tsuji, Yasushi

2014-02-05

We report, herein, the design, synthesis, and properties of new materials directed toward molecular electronics. A transition metal-containing insulated molecular wire was synthesized through the coordination polymerization of a Ru(II) porphyrin with an insulated bridging ligand of well-defined structure. The wire displayed not only high linearity and rigidity, but also high intramolecular charge mobility. Owing to the unique properties of the coordination bond, the interconversion between the monomer and polymer states was realized under a carbon monoxide atmosphere or UV irradiation. The results demonstrated a high potential of the metal-containing insulated molecular wire for applications in molecular electronics.

Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites.

PubMed

Tam, Lik-Ho; Wu, Chao

2017-10-13

The strong structural integrity of polymer nanocomposite is influenced in the moist environment; but the fundamental mechanism is unclear, including the basis for the interactions between the absorbed water molecules and the structure, which prevents us from predicting the durability of its applications across multiple scales. In this research, a molecular dynamics model of the epoxy/single-walled carbon nanotube (SWCNT) nanocomposite is constructed to explore the mechanism of the moisture effect, and an analysis of the molecular interactions is provided by focusing on the hydrogen bond (H-bond) network inside the nanocomposite structure. The simulations show that at low moisture concentration, the water molecules affect the molecular interactions by favorably forming the water-nanocomposite H-bonds and the small cluster, while at high concentration the water molecules predominantly form the water-water H-bonds and the large cluster. The water molecules in the epoxy matrix and the epoxy-SWCNT interface disrupt the molecular interactions and deteriorate the mechanical properties. Through identifying the link between the water molecules and the nanocomposite structure and properties, it is shown that the free volume in the nanocomposite is crucial for its structural integrity, which facilitates the moisture accumulation and the distinct material deteriorations. This study provides insights into the moisture-affected structure and properties of the nanocomposite from the nanoscale perspective, which contributes to the understanding of the nanocomposite long-term performance under the moisture effect.

Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites

PubMed Central

2017-01-01

The strong structural integrity of polymer nanocomposite is influenced in the moist environment; but the fundamental mechanism is unclear, including the basis for the interactions between the absorbed water molecules and the structure, which prevents us from predicting the durability of its applications across multiple scales. In this research, a molecular dynamics model of the epoxy/single-walled carbon nanotube (SWCNT) nanocomposite is constructed to explore the mechanism of the moisture effect, and an analysis of the molecular interactions is provided by focusing on the hydrogen bond (H-bond) network inside the nanocomposite structure. The simulations show that at low moisture concentration, the water molecules affect the molecular interactions by favorably forming the water-nanocomposite H-bonds and the small cluster, while at high concentration the water molecules predominantly form the water-water H-bonds and the large cluster. The water molecules in the epoxy matrix and the epoxy-SWCNT interface disrupt the molecular interactions and deteriorate the mechanical properties. Through identifying the link between the water molecules and the nanocomposite structure and properties, it is shown that the free volume in the nanocomposite is crucial for its structural integrity, which facilitates the moisture accumulation and the distinct material deteriorations. This study provides insights into the moisture-affected structure and properties of the nanocomposite from the nanoscale perspective, which contributes to the understanding of the nanocomposite long-term performance under the moisture effect. PMID:29027979

Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers

NASA Technical Reports Server (NTRS)

Fan, Wendy

2011-01-01

The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.

Structural, stability, and vibrational properties of BinPm clusters

NASA Astrophysics Data System (ADS)

Shen, Wanting; Han, Lihong; Liang, Dan; Zhang, Chunfang; Ruge, Quhe; Wang, Shumin; Lu, Pengfei

2018-04-01

An in-depth investigation is performed on stability mechanisms, electronic and optical properties of III-V semiconductor vapor phases clusters. First principles electronic structure calculations of CAM-B3LYP are performed on neutral BinPm (n + m ≤ 14) clusters. The geometrical evolution of all stable structures remains amorphous as the clusters size increases. Binding energies (BEs), energy gains and highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO-LUMO) gaps confirm that all four-atom structures of BinPm clusters have more stable optical properties. Orbitals composition and vibrational spectra of stable clusters are analyzed. Our calculations will contribute to the study of diluted bismuth alloys and compounds.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space.

PubMed

Lungu, Claudiu N; Diudea, Mircea V; Putz, Mihai V; Grudziński, Ireneusz P

2016-04-13

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space

PubMed Central

Lungu, Claudiu N.; Diudea, Mircea V.; Putz, Mihai V.; Grudziński, Ireneusz P.

2016-01-01

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose. PMID:27089324

Structure of Arabidopsis leaf starch is markedly altered following nocturnal degradation.

PubMed

Zhu, Fan; Bertoft, Eric; Wang, You; Emes, Michael; Tetlow, Ian; Seetharaman, Koushik

2015-03-06

Little is known about the thermal properties and internal molecular structure of transitory starch. In this study, granule morphology, thermal properties, and the cluster structure of Arabidopsis leaf starch at beginning and end of the light period were explored. The structural properties of building blocks and clusters were evaluated by using diverse chromatographic techniques. On the granular level, starch from end of day had larger granule size, thinner crystalline lamellae thickness, lower free surface energy of crystals, and lower tendency to retrograde than that from end of night. On the molecular level, the starch had lower amylose content, larger cluster size, and higher number of blocks per cluster at the end of day than at end of night. It is concluded that the core of the granules contains a more permanent molecular and less-ordered physical structure different from the transitory layers laid down around the core at daytime. Copyright © 2014 Elsevier Ltd. All rights reserved.

Influence of Molecular Conformations and Microstructure on the Optoelectronic Properties of Conjugated Polymers

PubMed Central

Botiz, Ioan; Stingelin, Natalie

2014-01-01

It is increasingly obvious that the molecular conformations and the long-range arrangement that conjugated polymers can adopt under various experimental conditions in bulk, solutions or thin films, significantly impact their resulting optoelectronic properties. As a consequence, the functionalities and efficiencies of resulting organic devices, such as field-effect transistors, light-emitting diodes, or photovoltaic cells, also dramatically change due to the close structure/property relationship. A range of structure/optoelectronic properties relationships have been investigated over the last few years using various experimental and theoretical methods, and, further, interesting correlations are continuously revealed by the scientific community. In this review, we discuss the latest findings related to the structure/optoelectronic properties interrelationships that exist in organic devices fabricated with conjugated polymers in terms of charge mobility, absorption, photoluminescence, as well as photovoltaic properties. PMID:28788568

Structure and properties of some chiralanes and chirolanes

NASA Astrophysics Data System (ADS)

Novak, Igor

2018-06-01

The molecular structures, spectra and properties of six chiralanes and chirolanes (approximately spheroidal, saturated, cage hydrocarbons) have been determined by density functional theory (DFT) quantum chemistry calculations. The main features determined are: molecular geometry, partial atomic charges, standard enthalpy of formation, IR, nuclear magnetic resonance (NMR) and circular dichroism (CD) spectra. On the basis of the calculated standard enthalpies of formation and highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gaps, we suggest that chiralanes/chirolanes are potential synthetic targets. We have calculated the anomalously large downfield 13C-NMR shifts for endohedral carbons in the spectra of [5.5] and [5.7]chiralanes.

Zeolites: Can they be synthesized by design

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

Davis, M.E.

1994-09-01

Zeolites and zeolite-like molecular sieves are crystalline oxides that have high surface-to-volume ratios and are able to recognize, discriminate, and organize molecules with differences of < 1 [angstrom]. The close connection between the atomic structure and macroscopic properties of these materials has led to uses in molecular recognition. For example, zeolites and zeolite-like molecular sieves can reveal marvelous molecular recognition specificity and sensitivity that can be applied to catalysis, separations technology, and chemical sensing. Additionally, they can serve as hosts to organize guest atoms and molecules that endow composite materials with optoelectric and electrochemical properties. Because of the high levelmore » of structural control necessary to create high-performance materials with zeolites or zeolite-like molecular sieves, the design and synthesis of these solids with specific architectures and properties are highly desired. Although this lofty goal is still elusive, advances have been made to allow the serious consideration of designing molecular sieves. Here, the author covers two aspects of this ongoing effort. First, he discusses the feasibility of designing pore architectures through the use of organic structure-directing agents. Second, he explores the possibility of creating zeolites through ''Lego chemistry.''« less

Structure and properties of fullerene molecular crystals with linear-scaling van der Waals density functional theory

NASA Astrophysics Data System (ADS)

Mostofi, Arash; Andrinopoulos, Lampros; Hine, Nicholas

2014-03-01

Fullerene molecular crystals are of technological promise for their use in heterojunction photovoltaic cells. An improved theoretical understanding of their structure and properties would be a step towards the rational design of new devices. Simulations based on density-functional theory (DFT) are invaluable for developing such insight, but standard semi-local functionals do not capture the important inter-molecular van der Waals (vdW) interactions in fullerene crystals. Furthermore the computational cost associated with the large unit cells needed are at the limit or beyond the capabilities of traditional DFT methods. In this work we overcome these limitations by using our implementation of a number of vdW-DFs in the ONETEP linear-scaling DFT code to study the structural properties of C60 molecular crystals. Powder neutron diffraction shows that the low-temperature Pa-3 phase is orientationally ordered with individual C60 units rotated around the [111] direction. We fully explore the energy landscape associated with the rotation angle and find two stable structures that are energetically very close, one of which corresponds to the experimentally observed structure. We further consider the effect of orientational disorder in very large supercells of thousands of atoms.

Quantitative structure-property relationship (correlation analysis) of phosphonic acid-based chelates in design of MRI contrast agent.

PubMed

Tiwari, Anjani K; Ojha, Himanshu; Kaul, Ankur; Dutta, Anupama; Srivastava, Pooja; Shukla, Gauri; Srivastava, Rakesh; Mishra, Anil K

2009-07-01

Nuclear magnetic resonance imaging is a very useful tool in modern medical diagnostics, especially when gadolinium (III)-based contrast agents are administered to the patient with the aim of increasing the image contrast between normal and diseased tissues. With the use of soft modelling techniques such as quantitative structure-activity relationship/quantitative structure-property relationship after a suitable description of their molecular structure, we have studied a series of phosphonic acid for designing new MRI contrast agent. Quantitative structure-property relationship studies with multiple linear regression analysis were applied to find correlation between different calculated molecular descriptors of the phosphonic acid-based chelating agent and their stability constants. The final quantitative structure-property relationship mathematical models were found as--quantitative structure-property relationship Model for phosphonic acid series (Model 1)--log K(ML) = {5.00243(+/-0.7102)}- MR {0.0263(+/-0.540)}n = 12 l r l = 0.942 s = 0.183 F = 99.165 quantitative structure-property relationship Model for phosphonic acid series (Model 2)--log K(ML) = {5.06280(+/-0.3418)}- MR {0.0252(+/- .198)}n = 12 l r l = 0.956 s = 0.186 F = 99.256.

Complementary study of molecular dynamics and domain sizes in heterogenous nanocomposites PBT/DA-C{sub 60} and PBT/TCNEO-C{sub 60}

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

Woźniak-Braszak, A., E-mail: abraszak@amu.edu.pl; Baranowski, M.; Jurga, K.

2014-05-28

A comprehensive study of molecular dynamics and structure in new heterogenous nanocomposites based on poly(butylene terephthalate) and nanoparticles C{sub 60} modified by n-decylamine or tetracyanoethylene oxide has been performed. The domain structure of new nanocomposites has been investigated by Fourier transform infrared spectroscopy, wide-angle X-ray scattering, and differential scanning calorimetry techniques. Solid-state {sup 1}H NMR techniques were used to study molecular dynamics and domain sizes in new nanocomposites. Information about the electronic properties of these nanocomposites was obtained by means of electron paramagnetic resonance method. It was shown that the structure and molecular dynamics of new nanocomposites were strongly dependentmore » on the properties and concentration of fullerene derivates.« less

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.

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.

Scanning tunneling microscopy of the formation, transformation, and property of oligothiophene self-organizations on graphite and gold surfaces.

PubMed

Yang, Zhi-Yong; Zhang, Hui-Min; Yan, Cun-Ji; Li, Shan-Shan; Yan, Hui-Juan; Song, Wei-Guo; Wan, Li-Jun

2007-03-06

Two alkyl-substituted dual oligothiophenes, quarterthiophene (4T)-trimethylene (tm)-octithiophene (8T) and 4T-tm-4T, were used to fabricate molecular structures on highly oriented pyrolytic graphite and Au(111) surfaces. The resulted structures were investigated by scanning tunneling microscopy. The 4T-tm-8T and 4T-tm-4T molecules self-organize into long-range ordered structures with linear and/or quasi-hexagonal patterns on highly oriented pyrolytic graphite at ambient temperature. Thermal annealing induced a phase transformation from quasi-hexagonal to linear in 4T-tm-8T adlayer. The molecules adsorbed on Au(111) surface in randomly folded and linear conformation. Based on scanning tunneling microscopy results, the structural models for different self-organizations were proposed. Scanning tunneling spectroscopy measurement showed the electronic property of individual molecules in the patterns. These results are significant in understanding the chemistry of molecular structure, including its formation, transformation, and electronic properties. They also help to fabricate oligothiophene assemblies with desired structures for future molecular devices.

Molecular interactions and structures in ethylene glycol-ethanol and ethylene glycol-water solutions at 303 K on densities, viscosities, and refractive indices data

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Ghatbandhe, A. S.

2014-01-01

Molecular interactions and structural fittings in binary ethylene glycol + ethanol (EGE, x EG = 0.4111-0.0418) and ethylene glycol + water (EGW, x EG = 0.1771-0.0133) mixtures were studied through the measurement of densities (ρ), viscosities (η), and refractive indices ( n D ) at 303.15 K. Excess viscosities (η E ), molar volumes ( V m ), excess molar volumes ( V {/m E }), and molar retractions ( R M ) of the both binary systems were computed from measured properties. The measured and computed properties have been used to understand the molecular interactions in unlike solvents and structural fittings in these binary mixtures.

AB INITIO Molecular Dynamics Simulations on Local Structure and Electronic Properties in Liquid MgxBi1-x Alloys

NASA Astrophysics Data System (ADS)

Hao, Qing-Hai; You, Yu-Wei; Kong, Xiang-Shan; Liu, C. S.

2013-03-01

The microscopic structure and dynamics of liquid MgxBi1-x(x = 0.5, 0.6, 0.7) alloys together with pure liquid Mg and Bi metals were investigated by means of ab initio molecular dynamics simulations. We present results of structure properties including pair correlation function, structural factor, bond-angle distribution function and bond order parameter, and their composition dependence. The dynamical and electronic properties have also been studied. The structure factor and pair correlation function are in agreement with the available experimental data. The calculated bond-angle distribution function and bond order parameter suggest that the stoichiometric composition Mg3Bi2 exhibits a different local structure order compared with other concentrations, which help us understand the appearance of the minimum electronic conductivity at this composition observed in previous experiments.

Skip residues modulate the structural properties of the myosin rod and guide thick filament assembly

DOE PAGES

Taylor, Keenan C.; Buvoli, Massimo; Korkmaz, Elif Nihal; ...

2015-07-06

The rod of sarcomeric myosins directs thick filament assembly and is characterized by the insertion of four skip residues that introduce discontinuities in the coiled-coil heptad repeats. We report in this paper that the regions surrounding the first three skip residues share high structural similarity despite their low sequence homology. Near each of these skip residues, the coiled-coil transitions to a nonclose-packed structure inducing local relaxation of the superhelical pitch. Moreover, molecular dynamics suggest that these distorted regions can assume different conformationally stable states. In contrast, the last skip residue region constitutes a true molecular hinge, providing C-terminal rod flexibility.more » Assembly of myosin with mutated skip residues in cardiomyocytes shows that the functional importance of each skip residue is associated with rod position and reveals the unique role of the molecular hinge in promoting myosin antiparallel packing. By defining the biophysical properties of the rod, the structures and molecular dynamic calculations presented here provide insight into thick filament formation, and highlight the structural differences occurring between the coiled-coils of myosin and the stereotypical tropomyosin. Finally, in addition to extending our knowledge into the conformational and biological properties of coiled-coil discontinuities, the molecular characterization of the four myosin skip residues also provides a guide to modeling the effects of rod mutations causing cardiac and skeletal myopathies.« less

Thermodynamic Control of Two-Dimensional Molecular Ionic Nanostructures on Metal Surfaces

DOE PAGES

Jeon, Seokmin; Doak, Peter W.; Sumpter, Bobby G.; ...

2016-07-26

Bulk molecular ionic solids exhibit fascinating electronic properties, including electron correlations, phase transitions and superconducting ground states. In contrast, few of these phenomena have so far been observed in low-dimensional molecular structures, including thin films, nanoparticles and molecular blends, not in the least because most of such structures have so far been composed of nearly closed-shell molecules. It is therefore desirable to develop low-dimensional molecular structures of ionic molecules toward fundamental studies and potential applications. Here we present detailed analysis of monolayer-thick structures of the canonical TTF-TCNQ (tetrathiafulvalene 7,7,8,8-tetracyanoquinodimethane) system grown on low-index gold and silver surfaces. The most distinctivemore » property of the epitaxial growth is the wide abundance of stable TTF/TCNQ ratios, in sharp contrast to the predominance of 1:1 ratio in the bulk. We propose the existence of the surface phase-diagram that controls the structures of TTF-TCNQ on the surfaces, and demonstrate phase-transitions that occur upon progressively increasing the density of TCNQ while keeping the surface coverage of TTF fixed. Based on direct observations, we propose the binding motif behind the stable phases and infer the dominant interactions that enable the existence of the rich spectrum of surface structures. Finally, we also show that the surface phase diagram will control the epitaxy beyond monolayer coverage. Multiplicity of stable surface structures, the corollary rich phase diagram and the corresponding phase-transitions present an interesting opportunity for low-dimensional molecular systems, particularly if some of the electronic properties of the bulk can be preserved or modified in the surface phases.« less

The mechanical properties of as-grown noncubic organic molecular crystals assessed by nanoindentation

DOE PAGES

Taw, Matthew R.; Yeager, John D.; Hooks, Daniel E.; ...

2017-06-19

Organic molecular crystals are often noncubic and contain significant steric hindrance within their structure to resist dislocation motion. Plastic deformation in these systems can be imparted during processing (tableting and comminution of powders), and the defect density impacts subsequent properties and performance. This paper measured the elastic and plastic properties of representative monoclinic, orthorhombic, and triclinic molecular crystalline structures using nanoindentation of as-grown sub-mm single crystals. The variation in modulus due to in-plane rotational orientation, relative to a Berkovich tip, was approximately equal to the variation of a given crystal at a fixed orientation. The onset of plasticity occurs consistentlymore » at shear stresses between 1 and 5% of the elastic modulus in all three crystal systems, and the hardness to modulus ratio suggests conventional Berkovich tips do not generate fully self-similar plastic zones in these materials. Finally, this provides guidance for mechanical models of tableting, machining, and property assessment of molecular crystals.« less

Signature properties of water: Their molecular electronic origins

PubMed Central

Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

2015-01-01

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

Structural elements and organization of the ancestral translational machinery

NASA Technical Reports Server (NTRS)

Rein, R.; Srinivasan, S.; Mcdonald, J.; Raghunathan, G.; Shibata, M.

1987-01-01

The molecular mechanisms of the primitive translational apparatus are discussed in the framework of present-day protein biosynthesis. The structural necessities of an early adaptor and the multipoint recognition properties of such an adaptor are investigated on the basis of structure/function relationships found in a contemporary system and a molecular model of the contemporary transpeptidation complex. A model of the tRNA(Tyr)-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed; the model is used to illustrate the required recognition properties of the ancestor aminoacyl synthetase.

pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe.

PubMed

Murugan, N Arul; Kongsted, Jacob; Ågren, Hans

2013-08-13

Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.

Machine learning for the structure–energy–property landscapes of molecular crystals† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04665k

PubMed Central

Yang, Jack; Campbell, Joshua E.; Day, Graeme M.; Ceriotti, Michele

2017-01-01

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol–1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure–property relations in molecular crystal engineering. PMID:29675175

Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites

DTIC Science & Technology

2016-06-08

conjugated polymers and composites by analysis of the structural determinants of the mechanical properties. We developed coarse-grained molecular...dynamics simulations that predicted the mechanical properties of conjugated polymers and polymer -fullerene composites. We elucidated the mechanical...We also determined the effect of cyclic stretching on the microstructure and mechanical properties of conjugated polymers . We used many of

The polysaccharide and low molecular weight components of Opuntia ficus indica cladodes: Structure and skin repairing properties.

PubMed

Di Lorenzo, Flaviana; Silipo, Alba; Molinaro, Antonio; Parrilli, Michelangelo; Schiraldi, Chiara; D'Agostino, Antonella; Izzo, Elisabetta; Rizza, Luisa; Bonina, Andrea; Bonina, Francesco; Lanzetta, Rosa

2017-02-10

The Opuntia ficus-indica multiple properties are reflected in the increasing interest of chemists in the identification of its natural components having pharmaceutical and/or cosmetical applications. Here we report the structural elucidation of Opuntia ficus-indica mucilage that highlighted the presence of components differing for their chemical nature and the molecular weight distribution. The high molecular weight components were identified as a linear galactan polymer and a highly branched xyloarabinan. The low molecular weight components were identified as lactic acid, D-mannitol, piscidic, eucomic and 2-hydroxy-4-(4'-hydroxyphenyl)-butanoic acids. A wound healing assay was performed in order to test the cicatrizing properties of the various components, highlighting the ability of these latter to fasten dermal regeneration using a simplified in vitro cellular model based on a scratched keratinocytes monolayer. The results showed that the whole Opuntia mucilage and the low molecular weight components are active in the wound repair. Copyright © 2016 Elsevier Ltd. All rights reserved.

Teaching Structure-Property Relationships: Investigating Molecular Structure and Boiling Point

ERIC Educational Resources Information Center

Murphy, Peter M.

2007-01-01

A concise, well-organized table of the boiling points of 392 organic compounds has facilitated inquiry-based instruction in multiple scientific principles. Many individual or group learning activities can be derived from the tabulated data of molecular structure and boiling point based on the instructor's education objectives and the students'…

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

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

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

PubMed

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-05

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

From the molecular structure to spectroscopic and material properties: computational investigation of a bent-core nematic liquid crystal.

PubMed

Greco, Cristina; Marini, Alberto; Frezza, Elisa; Ferrarini, Alberta

2014-05-19

We present a computational investigation of the nematic phase of the bent-core liquid crystal A131. We use an integrated approach that bridges density functional theory calculations of molecular geometry and torsional potentials to elastic properties through the molecular conformational and orientational distribution function. This unique capability to simultaneously access different length scales enables us to consistently describe molecular and material properties. We can reassign (13)C NMR chemical shifts and analyze the dependence of phase properties on molecular shape. Focusing on the elastic constants we can draw some general conclusions on the unconventional behavior of bent-core nematics and highlight the crucial role of a properly-bent shape. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular properties of food allergens.

PubMed

Breiteneder, Heimo; Mills, E N Clare

2005-01-01

Plant food allergens belong to a rather limited number of protein families and are also characterized by a number of biochemical and physicochemical properties, many of which are also shared by food allergens of animal origin. These include thermal stability and resistance to proteolysis, which are enhanced by an ability to bind ligands, such as metal ions, lipids, or steroids. Other types of lipid interaction, including membranes or other lipid structures, represent another feature that might promote the allergenic properties of certain food proteins. A structural feature clearly related to stability is intramolecular disulfide bonds alongside posttranslational modifications, such as N-glycosylation. Some plant food allergens, such as the cereal seed storage prolamins, are rheomorphic proteins with polypeptide chains that adopt an ensemble of secondary structures resembling unfolded or partially folded proteins. Other plant food allergens are characterized by the presence of repetitive structures, the ability to form oligomers, and the tendency to aggregate. A summary of our current knowledge regarding the molecular properties of food allergens is presented. Although we cannot as yet predict the allergenicity of a given food protein, understanding of the molecular properties that might predispose them to becoming allergens is an important first step and will undoubtedly contribute to the integrative allergenic risk assessment process being adopted by regulators.

Atomistic investigation of the structural, transport, and mechanical properties of Cu-Zr metallic glasses

NASA Astrophysics Data System (ADS)

Kumar, Mohit

The unique set of mechanical and magnetic properties possessed by metallic glasses has attracted a lot of recent scientific and technological interest. The development of new metallic glass alloys with improved manufacturability, enhanced properties and higher ductility relies on the fundamental understanding of the interconnections between their atomic structure, glass forming ability (GFA), transport properties, and elastic and plastic deformation mechanisms. This thesis is focused on finding these atomic structure-property relationships in Cu-Zr BMGs using molecular dynamics simulations. In the first study described herein, molecular dynamics simulations of the rapid solidification process over the Cu-Zr compositional domain were conducted to explore inter-dependencies of atomic transport and fragility, elasticity and structural ordering, and GFA. The second study investigated the atomic origins of serration events, which is the characteristic plastic deformation behaviour in BMGs. The combined results of this work suggest that GFA and ductility of metallic glasses could be compositionally tuned.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

PubMed

Deng, Lu; Du, Jincheng

2018-01-14

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Q n distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3 B and 4 B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Deng, Lu; Du, Jincheng

2018-01-01

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Understanding physicochemical properties changes from multi-scale structures of starch/CNT nanocomposite films.

PubMed

Liu, Siyuan; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing; Zhu, Jie

2017-11-01

From the view of multi-scale structures of hydroxypropyl starch (HPS)/carbon nanotube (CNT) nanocomposite films, the film physicochemical properties were affected by comprehensive factors including molecular interaction, short range molecular conformation, crystalline structure and aggregated structure. The less original HPS hydrogen bonding that was broken, less decreased order of HPS short range molecular conformation, lower film crystallinity and larger size of micro-ordered regions contributed to higher tensile strength and Young's modulus of the film with CNT content of 0.5% (g/g, CNT in HPS). The higher film overall crystallinity and larger size of micro-ordered regions of the film with CNT content of 0.05%-0.3% compared with those of control contributed to better film barrier property. The addition of CNT with the content of 0.05%-0.5% broke the original HPS hydrogen bonding and decreased the order of starch short range molecular conformation, which counteracted the positive effect of CNT on the thermal stability of the material, thus thermal degradation temperature of these nanocomposite films did not increase. But the sharp increase of film crystallinity increased film thermal degradation temperature. This study provided a better understanding of film physicochemical properties changes which guides to rational design of starch-based nanocomposite films for packaging and coating application. Copyright © 2017. Published by Elsevier B.V.

Electronic and transport properties of a molecular junction with asymmetric contacts.

PubMed

Tsai, M-H; Lu, T-H

2010-02-10

Asymmetric molecular junctions have been shown experimentally to exhibit a dual-conductance transport property with a pulse-like current-voltage characteristic, by Reed and co-workers. Using a recently developed first-principles integrated piecewise thermal equilibrium current calculation method and a gold-benzene-1-olate-4-thiolate-gold model molecular junction, this unusual transport property has been reproduced. Analysis of the electrostatics and the electronic structure reveals that the high-current state results from subtle bias induced charge transfer at the electrode-molecule contacts that raises molecular orbital energies and enhances the current-contributing molecular density of states and the probabilities of resonance tunneling of conduction electrons from one electrode to another.

QSAR modeling of cumulative environmental end-points for the prioritization of hazardous chemicals.

PubMed

Gramatica, Paola; Papa, Ester; Sangion, Alessandro

2018-01-24

The hazard of chemicals in the environment is inherently related to the molecular structure and derives simultaneously from various chemical properties/activities/reactivities. Models based on Quantitative Structure Activity Relationships (QSARs) are useful to screen, rank and prioritize chemicals that may have an adverse impact on humans and the environment. This paper reviews a selection of QSAR models (based on theoretical molecular descriptors) developed for cumulative multivariate endpoints, which were derived by mathematical combination of multiple effects and properties. The cumulative end-points provide an integrated holistic point of view to address environmentally relevant properties of chemicals.

Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

NASA Astrophysics Data System (ADS)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.

Many Molecular Properties from One Kernel in Chemical Space

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

Ramakrishnan, Raghunathan; von Lilienfeld, O. Anatole

We introduce property-independent kernels for machine learning modeling of arbitrarily many molecular properties. The kernels encode molecular structures for training sets of varying size, as well as similarity measures sufficiently diffuse in chemical space to sample over all training molecules. Corresponding molecular reference properties provided, they enable the instantaneous generation of ML models which can systematically be improved through the addition of more data. This idea is exemplified for single kernel based modeling of internal energy, enthalpy, free energy, heat capacity, polarizability, electronic spread, zero-point vibrational energy, energies of frontier orbitals, HOMOLUMO gap, and the highest fundamental vibrational wavenumber. Modelsmore » of these properties are trained and tested using 112 kilo organic molecules of similar size. Resulting models are discussed as well as the kernels’ use for generating and using other property models.« less

Correlation of the protein structure and gelling properties in dried egg white products.

PubMed

Handa, A; Hayashi, K; Shidara, H; Kuroda, N

2001-08-01

The relationship between protein structure and aggregation, as well as heat-induced gelling properties, of seven dried egg white (DEW) products was investigated. Strong correlations were found between average molecular weight and hydrophobicity plus surface SH groups of DEW-soluble protein aggregate (SPA). This suggests that hydrophobic interactions and disulfide bond formation between protein molecules were involved in the aggregation. The average molecular weight of DEW products with alkaline pHs was relatively higher than those with neutral pHs and the same degree of protein unfolding, probably because of more disulfide bond formation between protein molecules. In addition, strong correlations were found between hydrophobicity, surface SH groups plus average molecular weight of DEW-SPA, and physical properties of the gels from DEW products. These data indicated that controlling the aggregation of DEW proteins in the dry state is crucial to controlling the gelling properties of DEW.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

Essential Set of Molecular Descriptors for ADME Prediction in Drug and Environmental Chemical Space

EPA Science Inventory

Historically, the disciplines of pharmacology and toxicology have embraced quantitative structure-activity relationships (QSAR) and quantitative structure-property relationships (QSPR) to predict ADME properties or biological activities of untested chemicals. The question arises ...

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.

PubMed

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-14

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiC x O 6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations

NASA Astrophysics Data System (ADS)

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-01

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Effects of Molecular Structure in Macroscopic Mechanical Properties of an Advanced Polymer (LARC(sup TM)-SI)

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Hinkley, Jeffrey A.; Whitley, Karen S.; Gates, Thomas S.

2004-01-01

Mechanical testing of an advanced polymer resin with known variations in molecular weight was performed over a range of temperatures below the glass transition temperature. The elastic properties, inelastic elongation behavior, and notched tensile strength all as a function of molecular weight and test temperature were determined. It was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature.

On Topological Indices of Certain Families of Nanostar Dendrimers.

PubMed

Husin, Mohamad Nazri; Hasni, Roslan; Arif, Nabeel Ezzulddin; Imran, Muhammad

2016-06-24

A topological index of graph G is a numerical parameter related to G which characterizes its molecular topology and is usually graph invariant. In the field of quantitative structure-activity (QSAR)/quantitative structure-activity structure-property (QSPR) research, theoretical properties of the chemical compounds and their molecular topological indices such as the Randić connectivity index, atom-bond connectivity (ABC) index and geometric-arithmetic (GA) index are used to predict the bioactivity of different chemical compounds. A dendrimer is an artificially manufactured or synthesized molecule built up from the branched units called monomers. In this paper, the fourth version of ABC index and the fifth version of GA index of certain families of nanostar dendrimers are investigated. We derive the analytical closed formulas for these families of nanostar dendrimers. The obtained results can be of use in molecular data mining, particularly in researching the uniqueness of tested (hyper-branched) molecular graphs.

Molecular clouds and the large-scale structure of the galaxy

NASA Technical Reports Server (NTRS)

Thaddeus, Patrick; Stacy, J. Gregory

1990-01-01

The application of molecular radio astronomy to the study of the large-scale structure of the Galaxy is reviewed and the distribution and characteristic properties of the Galactic population of Giant Molecular Clouds (GMCs), derived primarily from analysis of the Columbia CO survey, and their relation to tracers of Population 1 and major spiral features are described. The properties of the local molecular interstellar gas are summarized. The CO observing programs currently underway with the Center for Astrophysics 1.2 m radio telescope are described, with an emphasis on projects relevant to future comparison with high-energy gamma-ray observations. Several areas are discussed in which high-energy gamma-ray observations by the EGRET (Energetic Gamma-Ray Experiment Telescope) experiment aboard the Gamma Ray Observatory will directly complement radio studies of the Milky Way, with the prospect of significant progress on fundamental issues related to the structure and content of the Galaxy.

QSPR modeling: graph connectivity indices versus line graph connectivity indices

PubMed

Basak; Nikolic; Trinajstic; Amic; Beslo

2000-07-01

Five QSPR models of alkanes were reinvestigated. Properties considered were molecular surface-dependent properties (boiling points and gas chromatographic retention indices) and molecular volume-dependent properties (molar volumes and molar refractions). The vertex- and edge-connectivity indices were used as structural parameters. In each studied case we computed connectivity indices of alkane trees and alkane line graphs and searched for the optimum exponent. Models based on indices with an optimum exponent and on the standard value of the exponent were compared. Thus, for each property we generated six QSPR models (four for alkane trees and two for the corresponding line graphs). In all studied cases QSPR models based on connectivity indices with optimum exponents have better statistical characteristics than the models based on connectivity indices with the standard value of the exponent. The comparison between models based on vertex- and edge-connectivity indices gave in two cases (molar volumes and molar refractions) better models based on edge-connectivity indices and in three cases (boiling points for octanes and nonanes and gas chromatographic retention indices) better models based on vertex-connectivity indices. Thus, it appears that the edge-connectivity index is more appropriate to be used in the structure-molecular volume properties modeling and the vertex-connectivity index in the structure-molecular surface properties modeling. The use of line graphs did not improve the predictive power of the connectivity indices. Only in one case (boiling points of nonanes) a better model was obtained with the use of line graphs.

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Graph Kernels for Molecular Similarity.

PubMed

Rupp, Matthias; Schneider, Gisbert

2010-04-12

Molecular similarity measures are important for many cheminformatics applications like ligand-based virtual screening and quantitative structure-property relationships. Graph kernels are formal similarity measures defined directly on graphs, such as the (annotated) molecular structure graph. Graph kernels are positive semi-definite functions, i.e., they correspond to inner products. This property makes them suitable for use with kernel-based machine learning algorithms such as support vector machines and Gaussian processes. We review the major types of kernels between graphs (based on random walks, subgraphs, and optimal assignments, respectively), and discuss their advantages, limitations, and successful applications in cheminformatics. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal engineering of giant molecules based on perylene diimide conjugated polyhedral oligomeric silsesquioxane nano-atom

NASA Astrophysics Data System (ADS)

Ren, He

Molecular architectures and topologies are found contributing to the formation of supramolecular structures of giant molecules. Dr. Cheng's research group developed a diverse of giant molecules via precisely controlled chemistry synthetic routes. These giant molecules can be categorized into several different families, namely giant surfactants, giant shape amphiphiles and giant polyhedron. By analyzing the hierarchical structures of these carefully designed and precisely synthesized giant molecules, the structural factors which affect, or even dominates, in some cases, the formation of supramolecular structures are revealed in these intensive researches. The results will further contribute to the understanding of dependence of supramolecular structures on molecular designs as well as molecular topology, and providing a practical solution to the scaling up of microscopic molecular functionalities to macroscopic material properties. Molecular Nano Particles (MNPs), including fullerene (C60), POSS, Polyoxometalate (POM) and proteins etc., is defined and applied as a specific type of building blocks in the design and synthesis of giant molecules. The persistence in shape and symmetry is considered as one of the major properties of MNPs. This persistence will support the construction of giant molecules for further supramolecular structures' study by introducing specific shapes, or precisely located side groups which will facilitate self-assembling behaviors with pre-programmed secondary interactions. Dictating material physical properties by its chemical composition is an attractive yet currently failed approach in the study of materials. However, the pursuit of determining material properties by microscopic molecular level properties is never seized, and found its solution when the idea of crystal engineering is raised: should each atom in the material is located exactly where it is designed to be and is properly bonded, the property of the material is hence determined. In such "bottom-up" approach, the precise fabrication of 2 nm 100 nm nanostructures, is of great research interest. In this thesis, crystal engineering of giant molecules based on PDI conjugated POSS Nano-Atom (PDI-BPOSS) nano-atoms via self-assembly is performed and studied. Herein, three different giant molecules were synthesized: shape amphiphile, m-phenyl-(PDI-BPOSS)2 (S1) and tetrahedron, R-(PDI-BPOSS)4 (S2) and S-(PDI-BPOSS)4 (S3). Single crystals were grown for S1 and S2, X-ray diffraction (XRD), Scanning Electron Microscopy (SEM) and transmission electron microscopy (TEM) were performed, and crystal structures of these samples were determined, while hexagonal superlattice without crystal order can be observed for S3 to exhibit crystal-like morphology.

Multifunctional receptor model for dioxin and related compound toxic action: possible thyroid hormone-responsive effector-linked site.

PubMed Central

McKinney, J D

1989-01-01

Molecular/theoretical modeling studies have revealed that thyroid hormones and toxic chlorinated aromatic hydrocarbons of environmental significance (for which dioxin or TCDD is the prototype) have similar structural properties that could be important in molecular recognition in biochemical systems. These molecular properties include a somewhat rigid, sterically accessible and polarizable aromatic ring and size-limited, hydrophobic lateral substituents, usually contained in opposite adjoining rings of a diphenyl compound. These molecular properties define the primary binding groups thought to be important in molecular recognition of both types of structures in biochemical systems. Similar molecular reactivities are supported by the demonstration of effective specific binding of thyroid hormones and chlorinated aromatic hydrocarbons with four different proteins, enzymes, or receptor preparations that are known or suspected to be involved in the expression of thyroid hormone activity. These binding interactions represent both aromatic-aromatic (stacking) and molecular cleft-type recognition processes. A multiple protein or multifunctional receptor-ligand binding mechanism model is proposed as a way of visualizing the details and possible role of both the stacking and cleft type molecular recognition factors in the expression of biological activity. The model suggests a means by which hormone-responsive effector-linked sites (possible protein-protein-DNA complexes) can maintain highly structurally specific control of hormone action. Finally, the model also provides a theoretical basis for the design and conduct of further biological experimentation on the molecular mechanism(s) of action of toxic chlorinated aromatic hydrocarbons and thyroid hormones. Images FIGURE 3. A FIGURE 3. B FIGURE 3. C FIGURE 3. D PMID:2551666

Molecular deformation mechanisms of the wood cell wall material.

PubMed

Jin, Kai; Qin, Zhao; Buehler, Markus J

2015-02-01

Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. Although earlier work has shown that the cellular structure of wood is a key factor that renders it excellent mechanical properties at light weight, the mechanical properties of the wood cell wall material itself still needs to be understood comprehensively. The wood cell wall material features a fiber reinforced composite structure, where cellulose fibrils act as stiff fibers, and hemicellulose and lignin molecules act as soft matrix. The angle between the fiber direction and the loading direction has been found to be the key factor controlling the mechanical properties. However, how the interactions between theses constitutive molecules contribute to the overall properties is still unclear, although the shearing between fibers has been proposed as a primary deformation mechanism. Here we report a molecular model of the wood cell wall material with atomistic resolution, used to assess the mechanical behavior under shear loading in order to understand the deformation mechanisms at the molecular level. The model includes an explicit description of cellulose crystals, hemicellulose, as well as lignin molecules arranged in a layered nanocomposite. The results obtained using this model show that the wood cell wall material under shear loading deforms in an elastic and then plastic manner. The plastic regime can be divided into two parts according to the different deformation mechanisms: yielding of the matrix and sliding of matrix along the cellulose surface. Our molecular dynamics study provides insights of the mechanical behavior of wood cell wall material at the molecular level, and paves a way for the multi-scale understanding of the mechanical properties of wood. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modeling Biophysical and Biological Properties From the Characteristics of the Molecular Electron Density, Electron Localization and Delocalization Matrices, and the Electrostatic Potential

PubMed Central

Matta*, Chérif F

2014-01-01

The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pKa's, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme–substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as “interacting quantum atoms (IQA)” energies which are expressible into an interaction matrix of two body terms (and diagonal one body “self” terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established. © 2014 The Author and the Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:24777743

Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix.

PubMed

Sugimoto, Naoki

2014-01-01

How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described. © 2014 Elsevier Inc. All rights reserved.

Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations

DOE PAGES

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; ...

2014-10-29

We report that the detailed structural and mechanical properties of a tetraoleoyl cardiolipin (TOCL) bilayer were determined using neutron spin echo (NSE) spectroscopy, small angle neutron and X-ray scattering (SANS and SAXS, respectively), and molecular dynamics (MD) simulations. We used MD simulations to develop a scattering density profile (SDP) model, which was then utilized to jointly refine SANS and SAXS data. In addition to commonly reported lipid bilayer structural parameters, component distributions were obtained, including the volume probability, electron density and neutron scattering length density.

Carbon Nanomembranes

NASA Astrophysics Data System (ADS)

Angelova, Polina; Gölzhäuser, Armin

2017-03-01

This chapter describes the formation and properties of one nanometer thick carbon nanomembranes (CNMs), made by electron induced cross-linking of aromatic self-assembled monolayers (SAMs). The cross-linked SAMs are robust enough to be released from the surface and placed on solid support or over holes as free-standing membranes. Annealing at 1000K transforms CNMs into graphene accompanied by a change of mechanical stiffness and electrical resistance. The developed fabrication approach is scalable and provides molecular level control over thickness and homogeneity of the produced CNMs. The mechanisms of electron-induced cross-linking process are discussed in details. A variety of polyaromatic thiols: oligophenyls as well as small and extended condensed polycyclic hydrocarbons have been successfully employed, demonstrating that the structural and functional properties of the resulting nanomembranes are strongly determined by the structure of molecular monolayers. The mechanical properties of CNMs (Young's modulus, tensile strength and prestress) are characterized by bulge testing. The interpretation of the bulge test data relates the Young's modulus to the properties of single molecules and to the structure of the pristine SAMs. The gas transport through the CNM is measured onto polydimethylsiloxane (PDMS) - thin film composite membrane. The established relationship of permeance and molecular size determines the molecular sieving mechanism of permeation through this ultrathin sheet.

Defect formation in fluoropolymer films at their condensation from a gas phase

NASA Astrophysics Data System (ADS)

Luchnikov, P. A.

2018-01-01

The questions of radiation defects, factors of influence of electronic high-frequency discharge plasma components on the molecular structure and properties of the fluoropolymer vacuum films synthesized on a substrate from a gas phase are considered. It is established that at sedimentation of fluoropolymer coverings from a gas phase in high-frequency discharge plasma in films there are radiation defects in molecular and supramolecular structure because of the influence of active plasma components which significantly influence their main properties.

Mechanical Properties of Organic Semiconductors for Stretchable, Highly Flexible, and Mechanically Robust Electronics.

PubMed

Root, Samuel E; Savagatrup, Suchol; Printz, Adam D; Rodriquez, Daniel; Lipomi, Darren J

2017-05-10

Mechanical deformability underpins many of the advantages of organic semiconductors. The mechanical properties of these materials are, however, diverse, and the molecular characteristics that permit charge transport can render the materials stiff and brittle. This review is a comprehensive description of the molecular and morphological parameters that govern the mechanical properties of organic semiconductors. Particular attention is paid to ways in which mechanical deformability and electronic performance can coexist. The review begins with a discussion of flexible and stretchable devices of all types, and in particular the unique characteristics of organic semiconductors. It then discusses the mechanical properties most relevant to deformable devices. In particular, it describes how low modulus, good adhesion, and absolute extensibility prior to fracture enable robust performance, along with mechanical "imperceptibility" if worn on the skin. A description of techniques of metrology precedes a discussion of the mechanical properties of three classes of organic semiconductors: π-conjugated polymers, small molecules, and composites. The discussion of each class of materials focuses on molecular structure and how this structure (and postdeposition processing) influences the solid-state packing structure and thus the mechanical properties. The review concludes with applications of organic semiconductor devices in which every component is intrinsically stretchable or highly flexible.

Novel Breast Cancer Therapeutics Based on Bacterial Cupredoxin

DTIC Science & Technology

2008-09-01

M. and Lim, C. (1999) Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the...crowding has structural effects on the folded ensemble of polypeptides. energy landscape theory excluded volume effect molecular simulations protein... molecular simulations (51). Thermo- dynamic properties such as the radius of gyration (Rg), shape parameters ( and S) (11), and the fraction of native

Molecular dynamics simulations: advances and applications

PubMed Central

Hospital, Adam; Goñi, Josep Ramon; Orozco, Modesto; Gelpí, Josep L

2015-01-01

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. PMID:26604800

New concepts for molecular magnets

NASA Astrophysics Data System (ADS)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super-paramagnetism and quasi one-dimensional magnets.

United polarizable multipole water model for molecular mechanics simulation

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

Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu

2015-07-07

We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interactionmore » site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.« less

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

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

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

Delocalization error and "functional tuning" in Kohn-Sham calculations of molecular properties.

PubMed

Autschbach, Jochen; Srebro, Monika

2014-08-19

Kohn-Sham theory (KST) is the "workhorse" of numerical quantum chemistry. This is particularly true for first-principles calculations of ground- and excited-state properties for larger systems, including electronic spectra, electronic dynamic and static linear and higher order response properties (including nonlinear optical (NLO) properties), conformational or dynamic averaging of spectra and response properties, or properties that are affected by the coupling of electron and nuclear motion. This Account explores the sometimes dramatic impact of the delocalization error (DE) and possible benefits from the use of long-range corrections (LC) and "tuning" of functionals in KST calculations of molecular ground-state and response properties. Tuning refers to a nonempirical molecule-specific determination of adjustable parameters in functionals to satisfy known exact conditions, for instance, that the energy of the highest occupied molecular orbital (HOMO) should be equal to the negative vertical ionization potential (IP) or that the energy as a function of fractional electron numbers should afford straight-line segments. The presentation is given from the viewpoint of a chemist interested in computations of a variety of molecular optical and spectroscopic properties and of a theoretician developing methods for computing such properties with KST. In recent years, the use of LC functionals, functional tuning, and quantifying the DE explicitly have provided valuable insight regarding the performance of KST for molecular properties. We discuss a number of different molecular properties, with examples from recent studies from our laboratory and related literature. The selected properties probe different aspects of molecular electronic structure. Electric field gradients and hyperfine coupling constants can be exquisitely sensitive to the DE because it affects the ground-state electron density and spin density distributions. For π-conjugated molecules, it is shown how the DE manifests itself either in too strong or too weak delocalization of localized molecular orbitals (LMOs). Optical rotation is an electric-magnetic linear response property that is calculated in a similar fashion as the electric polarizability, but it is more sensitive to approximations and can benefit greatly from tuning and small DE. Hyperpolarizabilities of π-conjugated "push-pull" systems are examples of NLO properties that can be greatly improved by tuning of range-separated exchange (RSE) functionals, in part due to improved charge-transfer excitation energies. On-going work on band gap predictions is also mentioned. The findings may provide clues for future improvements of KST because different molecular properties exhibit varying sensitivity to approximations in the electronic structure model. The utility of analyzing molecular properties and the impact of the DE in terms of LMOs, representing "chemist's orbitals" such as individual lone pairs and bonds, is highlighted.

PHYSICOCHEMICAL PROPERTY CALCULATIONS

EPA Science Inventory

Computer models have been developed to estimate a wide range of physical-chemical properties from molecular structure. The SPARC modeling system approaches calculations as site specific reactions (pKa, hydrolysis, hydration) and `whole molecule' properties (vapor pressure, boilin...

Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution.

PubMed

Carbó-Dorca, Ramon; Gallegos, Ana; Sánchez, Angel J

2009-05-01

Classical quantitative structure-properties relationship (QSPR) statistical techniques unavoidably present an inherent paradoxical computational context. They rely on the definition of a Gram matrix in descriptor spaces, which is used afterwards to reduce the original dimension via several possible kinds of algebraic manipulations. From there, effective models for the computation of unknown properties of known molecular structures are obtained. However, the reduced descriptor dimension causes linear dependence within the set of discrete vector molecular representations, leading to positive semi-definite Gram matrices in molecular spaces. To resolve this QSPR dimensionality paradox (QSPR DP) here is proposed to adopt as starting point the quantum QSPR (QQSPR) computational framework perspective, where density functions act as infinite dimensional descriptors. The fundamental QQSPR equation, deduced from employing quantum expectation value numerical evaluation, can be approximately solved in order to obtain models exempt of the QSPR DP. The substitution of the quantum similarity matrix by an empirical Gram matrix in molecular spaces, build up with the original non manipulated discrete molecular descriptor vectors, permits to obtain classical QSPR models with the same characteristics as in QQSPR, that is: possessing a certain degree of causality and explicitly independent of the descriptor dimension. 2008 Wiley Periodicals, Inc.

Advances in visual representation of molecular potentials.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.

A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships.

PubMed

Sahoo, Sagarika; Adhikari, Chandana; Kuanar, Minati; Mishra, Bijay K

2016-01-01

Synthesis of organic compounds with specific biological activity or physicochemical characteristics needs a thorough analysis of the enumerable data set obtained from literature. Quantitative structure property/activity relationships have made it simple by predicting the structure of the compound with any optimized activity. For that there is a paramount data set of molecular descriptors (MD). This review is a survey on the generation of the molecular descriptors and its probable applications in QSP/AR. Literatures have been collected from a wide class of research journals, citable web reports, seminar proceedings and books. The MDs were classified according to their generation. The applications of the MDs on the QSP/AR have also been reported in this review. The MDs can be classified into experimental and theoretical types, having a sub classification of the later into structural and quantum chemical descriptors. The structural parameters are derived from molecular graphs or topology of the molecules. Even the pixel of the molecular image can be used as molecular descriptor. In QSPR studies the physicochemical properties include boiling point, heat capacity, density, refractive index, molar volume, surface tension, heat of formation, octanol-water partition coefficient, solubility, chromatographic retention indices etc. Among biological activities toxicity, antimalarial activity, sensory irritant, potencies of local anesthetic, tadpole narcosis, antifungal activity, enzyme inhibiting activity are some important parameters in the QSAR studies. The classification of the MDs is mostly generic in nature. The application of the MDs in QSP/AR also has a generic link. Experimental MDs are more suitable in correlation analysis than the theoretical ones but are more expensive for generation. In advent of sophisticated computational tools and experimental design proliferation of MDs is inevitable, but for a highly optimized MD, studies on generation of MD is an unending process.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

The Role of Knowledge Structures in the Ability of Preservice Elementary Teachers to Diagnose a Child's Understanding of Molecular Kinetics

ERIC Educational Resources Information Center

Bischoff, Paul J.

2006-01-01

This study explored preservice teachers' (n = 25) knowledge structures and their mastery of content knowledge in relation to their ability to diagnose the strengths and weaknesses of a fourth grader's videotaped explanations of a scientific phenomenon, i.e., molecular kinetic properties of air. Participants' knowledge structures were analyzed…

How Molecular Structure Affects Mechanical Properties of an Advanced Polymer

NASA Technical Reports Server (NTRS)

Nicholson, Lee M.; Whitley, Karen S.; Gates, Thomas S.; Hinkley, Jeffrey A.

2000-01-01

density was performed over a range of temperatures below the glass transition temperature. The physical characterization, elastic properties and notched tensile strength all as a function of molecular weight and test temperature were determined. For the uncrosslinked SI material, it was shown that notched tensile strength is a strong function of both temperature and molecular weight, whereas stiffness is only a strong function of temperature. For the crosslinked PETI-SI material, it was shown that the effect of crosslinking significantly enhances the mechanical performance of the low molecular weight material; comparable to that exhibited by the high molecular weight material.

Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

NASA Astrophysics Data System (ADS)

Ellsworth-Bowers, Timothy P.

The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular cloud structures. This distance catalog of 1,802 objects across the Galactic plane represents the first large-scale analysis of clump-scale objects in a variety of Galactic environments. The Galactocentric positions of these objects begin to trace out the spiral structure of the Milky Way, and suggest that dense molecular gas settles nearer the Galactic midplane than tracers of less-dense gas such as CO. Physical properties computed from the DPDFs reveal that BGPS objects trace a continuum of scales within giant molecular clouds, and extend the scaling relationships known as Larson's Laws to lower-mass substructures. The results presented here represent the first step on the road to seeing the molecular content of the Milky Way as a forest rather than individual nearby trees.

Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

NASA Astrophysics Data System (ADS)

Yip, Hin-Lap

Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

Role of Sequence and Structural Polymorphism on the Mechanical Properties of Amyloid Fibrils

PubMed Central

Kim, Jae In; Na, Sungsoo; Eom, Kilho

2014-01-01

Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP) fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD) simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain). Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture. PMID:24551113

Electronic structure and optical properties of metal doped tetraphenylporphyrins

NASA Astrophysics Data System (ADS)

Shah, Esha V.; Roy, Debesh R.

2018-05-01

A density functional scrutiny on the structure, electronic and optical properties of metal doped tetraphenylporphyrins MTPP (M=Fe, Co, Ni) is performed. The structural stability of the molecules is evaluated based on the electronic parameters like HOMO-LUMO gap (HLG), chemical hardness (η) and binding energy of the central metal atom to the molecular frame etc. The computed UltraViolet-Visible (UV-Vis) optical absorption spectra for all the compounds are also compared. The molecular structures reported are the lowest energy configurations. The entire calculations are carried out with a widely reliable functional, viz. B3LYP with a popular basis set which includes a scaler relativistic effect, viz. LANL2DZ.

Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models

PubMed Central

Zhong, Yang; Warren, G. Lee; Patel, Sandeep

2014-01-01

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be −5.6±0.2 kcal/mole, in respectable agreement with the experimental value of −5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

Structure-Function-Property-Design Interplay in Biopolymers: Spider Silk

PubMed Central

Tokareva, Olena; Jacobsen, Matthew; Buehler, Markus; Wong, Joyce; Kaplan, David L.

2013-01-01

Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures, and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. PMID:23962644

p/n-Polarity of thiophene oligomers in photovoltaic cells: role of molecular vs. supramolecular properties.

PubMed

Ghosh, Tanwistha; Gopal, Anesh; Saeki, Akinori; Seki, Shu; Nair, Vijayakumar C

2015-04-28

Molecular and supramolecular properties play key roles in the optoelectronic properties and photovoltaic performances of organic materials. In the present work, we show how small changes in the molecular structure affect such properties, which in turn control the intrinsic and fundamental properties such as the p/n-polarity of organic semiconductors in bulk-heterojunction solar cells. Herein, we designed and synthesized two acceptor-donor-acceptor type semiconducting thiophene oligomers end-functionalized with oxazolone/isoxazolone derivatives (OT1 and OT2 respectively). The HOMO-LUMO energy levels of both derivatives were found to be positioned in such a way that they can act as electron acceptors to P3HT and electron donors to PCBM. However, OT1 functions as a donor (with PCBM) and OT2 as an acceptor (with P3HT) in BHJ photovoltaic cells, and their reverse roles results in either no or poor performance of the cells. Detailed studies using UV-vis absorption and fluorescence spectroscopy, time-correlated single photon counting, UV-photoelectron spectroscopy, density functional theory calculations, X-ray diffraction, and thermal gravimetric analysis proved that both molecular and supramolecular properties contributed equally but in a contrasting manner to the abovementioned observation. The obtained results were further validated by flash-photolysis time-resolved microwave conductivity studies which showed an excellent correlation between the structure, property, and device performances of the materials.

Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets.

PubMed

Bacle, Amélie; Gautier, Romain; Jackson, Catherine L; Fuchs, Patrick F J; Vanni, Stefano

2017-04-11

Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

PubMed

Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

2014-04-28

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

Studies on the self-catalyzed Knoevenagel condensation, characterization, DPPH radical scavenging activity, cytotoxicity, and molecular properties of 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones using single crystal XRD and DFT techniques

NASA Astrophysics Data System (ADS)

Suresh Kumar, G. S.; Antony Muthu Prabhu, A.; Bhuvanesh, N.

2014-10-01

We have studied the self-catalyzed Knoevenagel condensation, spectral characterization, DPPH radical scavenging activity, cytotoxicity, and molecular properties of 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones using single crystal XRD and DFT techniques. In the absence of any catalyst, a series of novel 5-arylidene-2,2-dimethyl-1,3-dioxane-4,6-diones were synthesized using Meldrum’s acid and formylphenoxyaliphatic acid(s) in water. These molecules are arranged in the dimer form through intermolecular H-bonding in the single crystal XRD structure. Compounds have better DPPH radical scavenging activity and cytotoxicity against A431 cancer cell line. The optimized molecular structure, natural bond orbital analysis, electrostatic potential map, HOMO-LUMO energies, molecular properties, and atomic charges of these molecules have been studied by performing DFT/B3LYP/3-21G(*) level of theory in gas phase.

Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

NASA Astrophysics Data System (ADS)

Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

2012-10-01

This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

Physicochemical properties of the modeled structure of astacin metalloprotease moulting enzyme NAS-36 and mapping the druggable allosteric space of Heamonchus contortus, Brugia malayi and Ceanorhabditis elegans via molecular dynamics simulation.

PubMed

Sharma, Om Prakash; Agrawal, Sonali; Kumar, M Suresh

2013-12-01

Nematodes represent the second largest phylum in the animal kingdom. It is the most abundant species (500,000) in the planet. It causes chronic, debilitating infections worldwide such as ascariasis, trichuriasis, hookworm, enterobiasis, strongyloidiasis, filariasis and trichinosis, among others. Molecular modeling tools can play an important role in the identification and structural investigation of molecular targets that can act as a vital candidate against filariasis. In this study, sequence analysis of NAS-36 from H. contortus (Heamonchus contortus), B. malayi (Brugia malayi) and C. elegans (Ceanorhabditis elegans) has been performed, in order to identify the conserved residues. Tertiary structure was developed for an insight into the molecular structure of the enzyme. Molecular Dynamics Simulation (MDS) studies have been carried out to analyze the stability and the physical properties of the proposed enzyme models in the H. contortus, B. malayi and C. elegans. Moreover, the drug binding sites have been mapped for inhibiting the function of NAS-36 enzyme. The molecular identity of this protease could eventually demonstrate how ex-sheathment is regulated, as well as provide a potential target of anthelmintics for the prevention of nematode infections.

Derivatives of Ergot-alkaloids: Molecular structure, physical properties, and structure-activity relationships

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.; Spiteller, Michael

2012-09-01

A comprehensive screening of fifteen functionalized Ergot-alkaloids, containing bulk aliphatic cyclic substituents at D-ring of the ergoline molecular skeleton was performed, studying their structure-active relationships and model interactions with α2A-adreno-, serotonin (5HT2A) and dopamine D3 (D3A) receptors. The accounted high affinity to the receptors binding loops and unusual bonding situations, joined with the molecular flexibility of the substituents and the presence of proton accepting/donating functional groups in the studied alkaloids, may contribute to further understanding the mechanisms of biological activity in vivo and in predicting their therapeutic potential in central nervous system (CNS), including those related the Schizophrenia. Since the presented correlation between the molecular structure and properties, was based on the comprehensively theoretical computational and experimental physical study on the successfully isolated derivatives, through using routine synthetic pathways in a relatively high yields, marked these derivatives as 'treasure' for further experimental and theoretical studied in areas such as: (a) pharmacological and clinical testing; (b) molecular-drugs design of novel psychoactive substances; (c) development of the analytical protocols for determination of Ergot-alkaloids through a functionalization of the ergoline-skeleton, and more.

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

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

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

2016-01-01

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

Unveiling the hybrid interface in polymer nanocomposites enclosing silsesquioxanes with tunable molecular structure: Spectroscopic, thermal and mechanical properties.

PubMed

D'Arienzo, Massimiliano; Diré, Sandra; Redaelli, Matteo; Borovin, Evgeny; Callone, Emanuela; Di Credico, Barbara; Morazzoni, Franca; Pegoretti, Alessandro; Scotti, Roberto

2018-02-15

Organic-inorganic nanobuilding blocks (NBBs) based on silsesquioxanes (SSQs) have potential applications as nanofillers, thermal stabilizers, and rheological modifiers, which can improve thermomechanical properties of polymer hosts. The possibility to tune both siloxane structure and pendant groups can promote compatibilization and peculiar interactions with a plethora of polymers. However, the control on SSQs molecular architecture and functionalities is usually delicate and requires careful synthetic details. Moreover, investigating the influence of NBBs loading and structure on the hybrid interface and, in turn, on the polymer chains mobility and mechanical properties, may be challenging, especially for low-loaded materials. Herein, we describe the preparation and characterization of polybutadiene (PB) nanocomposites using as innovative fillers thiol-functionalized SSQs nanobuilding blocks (SH-NBBs), with both tailorable functionality and structure. Swelling experiments and, more clearly, solid-state NMR, enlightened a remarkable effect of SH-NBBs on the molecular structure and mobility of the polymeric chains, envisaging the occurrence of chemical interactions at the hybrid interface. Finally, thermal and DMTA analyses revealed that nanocomposites, even containing very low filler loadings (i.e. 1, 3 wt%), exhibited enhanced thermomechanical properties, which seem to be connected not only to the loading, but also to the peculiar cage or ladder-like architecture of SH-NBBs. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-assembly into soft materials of molecules derived from naturallyoccurring fatty-acids

NASA Astrophysics Data System (ADS)

Zhang, Mohan

The self-assembly of molecular gelators has provided an attractive route for the construction of nanostructured materials with desired functionalities. A well-defined paradigm for the design of molecular gels is needed, but none has yet been established. One of the important challenges to defining this paradigm is the creation of structure-property correlations for gelators at different distance scales. This dissertation centers on gaining additional insights in the relationship between small changes in gelator structures derived from long-chain, naturally-occurring fatty acids and the properties of the corresponding gels. This approach offers a reasonable method to probe the rational design of molecular gelators. (Abstract shortened by ProQuest.).

Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

NASA Astrophysics Data System (ADS)

Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

2014-01-01

In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).

Structural, vibrational and theoretical studies of anilinium trichloroacetate: new hydrogen bonded molecular crystal with nonlinear optical properties.

PubMed

Tanak, H; Pawlus, K; Marchewka, M K; Pietraszko, A

2014-01-24

In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm(-1) and 3600-80 cm(-1) regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be d(eff)=0.70 d(eff) (KDP). Copyright © 2013 Elsevier B.V. All rights reserved.

Kinetic theory for the formation of diamond nanothreads with desired configurations: a strain-temperature controlled phase diagram.

PubMed

Gao, Junfeng; Zhang, Gang; Yakobson, Boris I; Zhang, Yong-Wei

2018-05-24

Diamond nanothreads (DNTs) are a brand-new one-dimensional carbon nanomaterial that was synthesized recently by compressing benzene. Compared with sp2 carbon nanotubes, DNTs may possess a much higher interfacial load-transfer ability. However, previous studies have shown that the mechanical properties of DNTs are highly sensitive to the composition of Stone-Wales (SW) transformed sites. Up to now, it remained unclear what roles SWs play in the structure stability and how to engineer its molecular structure for novel mechanical properties. Using ab initio calculations, here we show that the most stable structure of a DNT is composed of alternative SW and hydrogenated carbon nanotube (3,0) units, suggesting that SW plays an essential role in stabilizing DNT. Interestingly, we found that the SW transition barrier is a nearly linear function of the applied strain, enabling strain engineering of its molecular structure. To do so, we propose a strain-temperature-stretching rate phase diagram to guide the construction of desired molecular structures to achieve superplastic behavior of DNTs. Our findings not only enrich our understanding of this novel carbon material, but also provide a strategy to control its structural and mechanical properties for novel applications, such as energy absorption, energy storage and materials reinforcement.

Quantitative structure-property relationships for octanol-water partition coefficients of polybrominated diphenyl ethers.

PubMed

Li, Linnan; Xie, Shaodong; Cai, Hao; Bai, Xuetao; Xue, Zhao

2008-08-01

Theoretical molecular descriptors were tested against logK(OW) values for polybrominated diphenyl ethers (PBDEs) using the Partial Least-Squares Regression method which can be used to analyze data with many variables and few observations. A quantitative structure-property relationship (QSPR) model was successfully developed with a high cross-validated value (Q(cum)(2)) of 0.961, indicating a good predictive ability and stability of the model. The predictive power of the QSPR model was further cross-validated. The values of logK(OW) for PBDEs are mainly governed by molecular surface area, energy of the lowest unoccupied molecular orbital and the net atomic charges on the oxygen atom. All these descriptors have been discussed to interpret the partitioning mechanism of PBDE chemicals. The bulk property of the molecules represented by molecular surface area is the leading factor, and K(OW) values increase with the increase of molecular surface area. Higher energy of the lowest unoccupied molecular orbital and higher net atomic charge on the oxygen atom of PBDEs result in smaller K(OW). The energy of the lowest unoccupied molecular orbital and the net atomic charge on PBDEs oxygen also play important roles in affecting the partition of PBDEs between octanol and water by influencing the interactions between PBDEs and solvent molecules.

Structural similarity based kriging for quantitative structure activity and property relationship modeling.

PubMed

Teixeira, Ana L; Falcao, Andre O

2014-07-28

Structurally similar molecules tend to have similar properties, i.e. closer molecules in the molecular space are more likely to yield similar property values while distant molecules are more likely to yield different values. Based on this principle, we propose the use of a new method that takes into account the high dimensionality of the molecular space, predicting chemical, physical, or biological properties based on the most similar compounds with measured properties. This methodology uses ordinary kriging coupled with three different molecular similarity approaches (based on molecular descriptors, fingerprints, and atom matching) which creates an interpolation map over the molecular space that is capable of predicting properties/activities for diverse chemical data sets. The proposed method was tested in two data sets of diverse chemical compounds collected from the literature and preprocessed. One of the data sets contained dihydrofolate reductase inhibition activity data, and the second molecules for which aqueous solubility was known. The overall predictive results using kriging for both data sets comply with the results obtained in the literature using typical QSPR/QSAR approaches. However, the procedure did not involve any type of descriptor selection or even minimal information about each problem, suggesting that this approach is directly applicable to a large spectrum of problems in QSAR/QSPR. Furthermore, the predictive results improve significantly with the similarity threshold between the training and testing compounds, allowing the definition of a confidence threshold of similarity and error estimation for each case inferred. The use of kriging for interpolation over the molecular metric space is independent of the training data set size, and no reparametrizations are necessary when more compounds are added or removed from the set, and increasing the size of the database will consequentially improve the quality of the estimations. Finally it is shown that this model can be used for checking the consistency of measured data and for guiding an extension of the training set by determining the regions of the molecular space for which new experimental measurements could be used to maximize the model's predictive performance.

Complementary molecular information changes our perception of food web structure

PubMed Central

Wirta, Helena K.; Hebert, Paul D. N.; Kaartinen, Riikka; Prosser, Sean W.; Várkonyi, Gergely; Roslin, Tomas

2014-01-01

How networks of ecological interactions are structured has a major impact on their functioning. However, accurately resolving both the nodes of the webs and the links between them is fraught with difficulties. We ask whether the new resolution conferred by molecular information changes perceptions of network structure. To probe a network of antagonistic interactions in the High Arctic, we use two complementary sources of molecular data: parasitoid DNA sequenced from the tissues of their hosts and host DNA sequenced from the gut of adult parasitoids. The information added by molecular analysis radically changes the properties of interaction structure. Overall, three times as many interaction types were revealed by combining molecular information from parasitoids and hosts with rearing data, versus rearing data alone. At the species level, our results alter the perceived host specificity of parasitoids, the parasitoid load of host species, and the web-wide role of predators with a cryptic lifestyle. As the northernmost network of host–parasitoid interactions quantified, our data point exerts high leverage on global comparisons of food web structure. However, how we view its structure will depend on what information we use: compared with variation among networks quantified at other sites, the properties of our web vary as much or much more depending on the techniques used to reconstruct it. We thus urge ecologists to combine multiple pieces of evidence in assessing the structure of interaction webs, and suggest that current perceptions of interaction structure may be strongly affected by the methods used to construct them. PMID:24449902

Molecular Modeling of Ammonium, Calcium, Sulfur, and Sodium Lignosulphonates in Acid and Basic Aqueous Environments

NASA Astrophysics Data System (ADS)

Salazar Valencia, P. J.; Bolívar Marinez, L. E.; Pérez Merchancano, S. T.

2015-12-01

Lignosulphonates (LS), also known as lignin sulfonates or sulfite lignin, are lignins in sulfonated forms, obtained from the "sulfite liquors," a residue of the wood pulp extraction process. Their main utility lies in its wide range of properties, they can be used as additives, dispersants, binders, fluxing, binder agents, etc. in fields ranging from food to fertilizer manufacture and even as agents in the preparation of ion exchange membranes. Since they can be manufactured relatively easy and quickly, and that its molecular size can be manipulated to obtain fragments of very low molecular weight, they are used as transport agents in the food industry, cosmetics, pharmaceutical and drug development, and as molecular elements for the treatment of health problems. In this paper, we study the electronic structural and optical characteristics of LS incorporating ammonium, sulfur, calcium, and sodium ions in acidic and basic aqueous media in order to gain a better understanding of their behavior and the very interesting properties exhibit. The studies were performed using the molecular modeling program HyperChem 5 using the semiempirical method PM3 of the NDO Family (neglect of differential overlap), to calculate the structural properties. We calculated the electronic and optical properties using the semiempirical method ZINDO / CI.

Structural characteristics of the molecular species of tetraacylglycerols in lesquerella (Physaria fendleri) oil elucidated by mass spectrometry

USDA-ARS?s Scientific Manuscript database

The structure and ratios of regioisomers of the molecular species of tetraacylglycerols affect their physical properties. They were elucidated by ESI mass spectrometry of the lithium adducts of tetraacylglycerols from the HPLC fractions of lesquerella oil. The contents of acyl and acylacyl chains at...

Atomically precise edge chlorination of nanographenes and its application in graphene nanoribbons

PubMed Central

Tan, Yuan-Zhi; Yang, Bo; Parvez, Khaled; Narita, Akimitsu; Osella, Silvio; Beljonne, David; Feng, Xinliang; Müllen, Klaus

2013-01-01

Chemical functionalization is one of the most powerful and widely used strategies to control the properties of nanomaterials, particularly in the field of graphene. However, the ill-defined structure of the present functionalized graphene inhibits atomically precise structural characterization and structure-correlated property modulation. Here we present a general edge chlorination protocol for atomically precise functionalization of nanographenes at different scales from 1.2 to 3.4 nm and its application in graphene nanoribbons. The well-defined edge chlorination is unambiguously confirmed by X-ray single-crystal analysis, which also discloses the characteristic non-planar molecular shape and detailed bond lengths of chlorinated nanographenes. Chlorinated nanographenes and graphene nanoribbons manifest enhanced solution processability associated with decreases in the optical band gap and frontier molecular orbital energy levels, exemplifying the structure-correlated property modulation by precise edge chlorination. PMID:24212200

When Do Students Recognize Relationships between Molecular Structure and Properties? A Longitudinal Comparison of the Impact of Traditional and Transformed Curricula

ERIC Educational Resources Information Center

Underwood, Sonia M.; Reyes-Gastelum, David; Cooper, Melanie M.

2016-01-01

The ability to use a chemical structure to predict and explain phenomenon is essential to a robust understanding of chemistry; however, previous research has shown that students find it difficult to make the connection between structure and properties. In this study we examine how student recognition of the connections between structure and…

Estimation of Melting Points of Organics.

PubMed

Yalkowsky, Samuel H; Alantary, Doaa

2018-05-01

Unified physicochemical property estimation relationships is a system of empirical and theoretical relationships that relate 20 physicochemical properties of organic molecules to each other and to chemical structure. Melting point is a key parameter in the unified physicochemical property estimation relationships scheme because it is a determinant of several other properties including vapor pressure, and solubility. This review describes the first-principals calculation of the melting points of organic compounds from structure. The calculation is based on the fact that the melting point, T m , is equal to the ratio of the heat of melting, ΔH m , to the entropy of melting, ΔS m . The heat of melting is shown to be an additive constitutive property. However, the entropy of melting is not entirely group additive. It is primarily dependent on molecular geometry, including parameters which reflect the degree of restriction of molecular motion in the crystal to that of the liquid. Symmetry, eccentricity, chirality, flexibility, and hydrogen bonding, each affect molecular freedom in different ways and thus make different contributions to the total entropy of fusion. The relationships of these entropy determining parameters to chemical structure are used to develop a reasonably accurate means of predicting the melting points over 2000 compounds. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Effects of styrene unit on molecular conformation and spectral properties of CNsbnd PhCHdbnd NPhCHdbnd CHPhsbnd CN

NASA Astrophysics Data System (ADS)

Fang, Zhengjun; Wu, Feng; Jiao, Yingchun; Wang, Nanfang; Au, Chaktong; Cao, Chenzhong; Yi, Bing

2018-05-01

Compound CN-PhCH=NPhCH=CHPh-CN with both stilbene and benzylidene aniline units was synthesized, and studied from the viewpoint of molecular conformation and spectroscopic property by a combined use of experimental and computational methods. The maximum UV absorption wavelength (λmax) of the compound in ethanol, acetonitrile, chloroform and cyclohexane solvents were measured, and the 13C NMR chemical shift value δC(Cdbnd N) in chloroform-d was determined. The crystal structure of the compound was determined by X-ray diffraction. The frontier molecular orbital was calculated by density functional theory method. The results show that the UV absorption spectrum of the titled compound is similar to those of Schiff bases, while there is a larger red shift of λmax comparing to that of CN-PhCH=NPh-CN. Moreover, the molecular configuration of the titled compound relative to Cdbnd N is anti-form, having a more obvious twisted structure. The spectral and structural behaviors are further supported by the results of frontier molecular orbital analyses, NBO, electrostatic potentials and TD-DFT calculations. The study provides deeper insights into the molecular conformation of Schiff bases.

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.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

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

Gao, Weimin; Niu, Haitao; Lin, Tong

2014-01-28

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform externalmore » electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

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

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu; Yang, Mo

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heatmore » transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.« less

Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.

A Group Contribution Method for Estimating Cetane and Octane Numbers

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

Kubic, William Louis

Much of the research on advanced biofuels is devoted to the study of novel chemical pathways for converting nonfood biomass into liquid fuels that can be blended with existing transportation fuels. Many compounds under consideration are not found in the existing fuel supplies. Often, the physical properties needed to assess the viability of a potential biofuel are not available. The only reliable information available may be the molecular structure. Group contribution methods for estimating physical properties from molecular structure have been used for more than 60 years. The most common application is estimation of thermodynamic properties. More recently, group contributionmore » methods have been developed for estimating rate dependent properties including cetane and octane numbers. Often, published group contribution methods are limited in terms of types of function groups and range of applicability. In this study, a new, broadly-applicable group contribution method based on an artificial neural network was developed to estimate cetane number research octane number, and motor octane numbers of hydrocarbons and oxygenated hydrocarbons. The new method is more accurate over a greater range molecular weights and structural complexity than existing group contribution methods for estimating cetane and octane numbers.« less

Black Carbon (Biochar) In Water/Soil Environments: Molecular Structure, Sorption, Stability, and Potential Risk.

PubMed

Lian, Fei; Xing, Baoshan

2017-12-05

Black carbon (BC) is ubiquitous in the environments and participates in various biogeochemical processes. Both positive and negative effects of BC (especially biochar) on the ecosystem have been identified, which are mainly derived from its diverse physicochemical properties. Nevertheless, few studies systematically examined the linkage between the evolution of BC molecular structure with the resulted BC properties, environmental functions as well as potential risk, which is critical for understanding the BC environmental behavior and utilization as a multifunctional product. Thus, this review highlights the molecular structure evolution of BC during pyrolysis and the impact of BC physicochemical properties on its sorption behavior, stability, and potential risk in terrestrial and aqueous ecosystems. Given the wide application of BC and its important role in biogeochemical processes, future research should focus on the following: (1) establishing methodology to more precisely predict and design BC properties on the basis of pyrolysis and phase transformation of biomass; (2) developing an assessment system to evaluate the long-term effect of BC on stabilization and bioavailability of contaminants, agrochemicals, and nutrient elements in soils; and (3) elucidating the interaction mechanisms of BC with plant roots, microorganisms, and soil components.

Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

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

Hajilar, Shahin, E-mail: shajilar@iastate.edu; Shafei, Behrouz, E-mail: shafei@iastate.edu

The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanicalmore » properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates. - Graphical abstract: Fracture mechanism of portlandite under uniaxial strain in the z-direction. - Highlights: • The structural, thermal, and mechanical properties of portlandite are investigated. • The coefficients of thermal expansion are determined. • The stress-strain relationships are studied in three orthogonal directions. • The effects of temperature and strain rate on mechanical properties are examined. • The plastic energy required for fracture in the crystalline structure is reported.« less

Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Androulaki, Eleni; Vergadou, Niki; Ramos, Javier; Economou, Ioannis G.

2012-06-01

Molecular dynamics (MD) simulations have been performed in order to investigate the properties of [C n mim+][Tf2N-] (n = 4, 8, 12) ionic liquids (ILs) in a wide temperature range (298.15-498.15 K) and at atmospheric pressure (1 bar). A previously developed methodology for the calculation of the charge distribution that incorporates ab initio quantum mechanical calculations based on density functional theory (DFT) was used to calculate the partial charges for the classical molecular simulations. The wide range of time scales that characterize the segmental dynamics of these ILs, especially at low temperatures, required very long MD simulations, on the order of several tens of nanoseconds, to calculate the thermodynamic (density, thermal expansion, isothermal compressibility), structural (radial distribution functions between the centers of mass of ions and between individual sites, radial-angular distribution functions) and dynamic (relaxation times of the reorientation of the bonds and the torsion angles, self-diffusion coefficients, shear viscosity) properties. The influence of the temperature and the cation's alkyl chain length on the above-mentioned properties was thoroughly investigated. The calculated thermodynamic (primary and derivative) and structural properties are in good agreement with the experimental data, while the extremely sluggish dynamics of the ILs under study renders the calculation of their transport properties a very complicated and challenging task, especially at low temperatures.

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

PubMed Central

Fujimoto, Takeshi; Nakano, Shu-ichi; Miyoshi, Daisuke; Sugimoto, Naoki

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

"Nonspecific" cholinesterase and acetylcholinesterase in rat tissues: molecular forms, structural and catalytic properties, and significance of the two enzyme systems.

PubMed Central

Vigny, M; Gisiger, V; Massoulié, J

1978-01-01

"Nonspecific" cholinesterase (acylcholine acylhydrolase; EC 3.1.1.8) from various rat tissues has been found to exist in several stable molecular forms that appear as exact counterparts of molecular forms of acetylcholinesterase (acetylcholine hydrolase; EC 3.1.1.7). The sedimentation pattern of cholinesterase was similar to that of acetylcholinesterase with a small but significant shift between the sedimentation coefficients of the corresponding forms. Extraction yields in different media also demonstrated a close parallelism between the two enzyme systems. Other properties, such as thermal stability and catalytic characteristics, indicated both differences and similarities. In spite of the structural resemblance implied by their physicochemical properties, cholinesterase did not crossreact with antibodies against acetylcholinesterase. The nature of the relationships revealed by these studies and their bearing on the physiological significance of cholinesterases are discussed. PMID:78492

A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

NASA Technical Reports Server (NTRS)

Foley, Henry C.

1990-01-01

The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.

Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

NASA Astrophysics Data System (ADS)

Guerrero, Carlo L.; Perlado, Jose M.

2016-03-01

In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

Cation solvation with quantum chemical effects modeled by a size-consistent multi-partitioning quantum mechanics/molecular mechanics method.

PubMed

Watanabe, Hiroshi C; Kubillus, Maximilian; Kubař, Tomáš; Stach, Robert; Mizaikoff, Boris; Ishikita, Hiroshi

2017-07-21

In the condensed phase, quantum chemical properties such as many-body effects and intermolecular charge fluctuations are critical determinants of the solvation structure and dynamics. Thus, a quantum mechanical (QM) molecular description is required for both solute and solvent to incorporate these properties. However, it is challenging to conduct molecular dynamics (MD) simulations for condensed systems of sufficient scale when adapting QM potentials. To overcome this problem, we recently developed the size-consistent multi-partitioning (SCMP) quantum mechanics/molecular mechanics (QM/MM) method and realized stable and accurate MD simulations, using the QM potential to a benchmark system. In the present study, as the first application of the SCMP method, we have investigated the structures and dynamics of Na + , K + , and Ca 2+ solutions based on nanosecond-scale sampling, a sampling 100-times longer than that of conventional QM-based samplings. Furthermore, we have evaluated two dynamic properties, the diffusion coefficient and difference spectra, with high statistical certainty. Furthermore the calculation of these properties has not previously been possible within the conventional QM/MM framework. Based on our analysis, we have quantitatively evaluated the quantum chemical solvation effects, which show distinct differences between the cations.

Dielectric Properties of Piezoelectric Polyimides

NASA Technical Reports Server (NTRS)

Ounaies, Z.; Young, J. A.; Simpson, J. O.; Farmer, B. L.

1997-01-01

Molecular modeling and dielectric measurements are being used to identify mechanisms governing piezoelectric behavior in polyimides such as dipole orientation during poling, as well as degree of piezoelectricity achievable. Molecular modeling on polyimides containing pendant, polar nitrile (CN) groups has been completed to determine their remanent polarization. Experimental investigation of their dielectric properties evaluated as a function of temperature and frequency has substantiated numerical predictions. With this information in hand, we are then able to suggest changes in the molecular structures, which will then improve upon the piezoelectric response.

A molecular dynamics study of polymer/graphene interfacial systems

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

Rissanou, Anastassia N.; Harmandaris, Vagelis

2014-05-15

Graphene based polymer nanocomposites are hybrid materials with a very broad range of technological applications. In this work, we study three hybrid polymer/graphene interfacial systems (polystyrene/graphene, poly(methyl methacrylate)/graphene and polyethylene/graphene) through detailed atomistic molecular dynamics (MD) simulations. Density profiles, structural characteristics and mobility aspects are being examined at the molecular level for all model systems. In addition, we compare the properties of the hybrid systems to the properties of the corresponding bulk ones, as well as to theoretical predictions.

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

PubMed

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

Evaluating frontier orbital energy and HOMO/LUMO gap with descriptors from density functional reactivity theory.

PubMed

Huang, Ying; Rong, Chunying; Zhang, Ruiqin; Liu, Shubin

2017-01-01

Wave function theory (WFT) and density functional theory (DFT)-the two most popular solutions to electronic structure problems of atoms and molecules-share the same origin, dealing with the same subject yet using distinct methodologies. For example, molecular orbitals are artifacts in WFT, whereas in DFT, electron density plays the dominant role. One question that needs to be addressed when using these approaches to appreciate properties related to molecular structure and reactivity is if there is any link between the two. In this work, we present a piece of strong evidence addressing that very question. Using five polymeric systems as illustrative examples, we reveal that using quantities from DFT such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, Onicescu information energy, Rényi entropy, etc., one is able to accurately evaluate orbital-related properties in WFT like frontier orbital energies and the HOMO (highest occupied molecular orbital)/LUMO (lowest unoccupied molecular orbital) gap. We verified these results at both the whole molecule level and the atoms-in-molecules level. These results provide compelling evidence suggesting that WFT and DFT are complementary to each other, both trying to comprehend the same properties of the electronic structure and molecular reactivity from different perspectives using their own characteristic vocabulary. Hence, there should be a bridge or bridges between the two approaches.

Correlating Single Crystal Structure, Nanomechanical, and Bulk Compaction Behavior of Febuxostat Polymorphs.

PubMed

Yadav, Jayprakash A; Khomane, Kailas S; Modi, Sameer R; Ugale, Bharat; Yadav, Ram Naresh; Nagaraja, C M; Kumar, Navin; Bansal, Arvind K

2017-03-06

Febuxostat exhibits unprecedented solid forms with a total of 40 polymorphs and pseudopolymorphs reported. Polymorphs differ in molecular arrangement and conformation, intermolecular interactions, and various physicochemical properties, including mechanical properties. Febuxostat Form Q (FXT Q) and Form H1 (FXT H1) were investigated for crystal structure, nanomechanical parameters, and bulk deformation behavior. FXT Q showed greater compressibility, densification, and plastic deformation as compared to FXT H1 at a given compaction pressure. Lower mechanical hardness of FXT Q (0.214 GPa) as compared to FXT H1 (0.310 GPa) was found to be consistent with greater compressibility and lower mean yield pressure (38 MPa) of FXT Q. Superior compaction behavior of FXT Q was attributed to the presence of active slip systems in crystals which offered greater plastic deformation. By virtue of greater compressibility and densification, FXT Q showed higher tabletability over FXT H1. Significant correlation was found with anticipation that the preferred orientation of molecular planes into a crystal lattice translated nanomechanical parameters to a bulk compaction process. Moreover, prediction of compactibility of materials based on true density or molecular packing should be carefully evaluated, as slip-planes may cause deviation in the structure-property relationship. This study supported how molecular level crystal structure confers a bridge between particle level nanomechanical parameters and bulk level deformation behavior.

Deformation micromechanisms of collagen fibrils under uniaxial tension

PubMed Central

Tang, Yuye; Ballarini, Roberto; Buehler, Markus J.; Eppell, Steven J.

2010-01-01

Collagen, an essential building block of connective tissues, possesses useful mechanical properties due to its hierarchical structure. However, little is known about the mechanical properties of collagen fibril, an intermediate structure between the collagen molecule and connective tissue. Here, we report the results of systematic molecular dynamics simulations to probe the mechanical response of initially unflawed finite size collagen fibrils subjected to uniaxial tension. The observed deformation mechanisms, associated with rupture and sliding of tropocollagen molecules, are strongly influenced by fibril length, width and cross-linking density. Fibrils containing more than approximately 10 molecules along their length and across their width behave as representative volume elements and exhibit brittle fracture. Shorter fibrils experience a more graceful ductile-like failure. An analytical model is constructed and the results of the molecular modelling are used to find curve-fitted expressions for yield stress, yield strain and fracture strain as functions of fibril structural parameters. Our results for the first time elucidate the size dependence of mechanical failure properties of collagen fibrils. The associated molecular deformation mechanisms allow the full power of traditional material and structural engineering theory to be applied to our understanding of the normal and pathological mechanical behaviours of collagenous tissues under load. PMID:19897533

Fibrin Formation, Structure and Properties

PubMed Central

Weisel, John W.; Litvinov, Rustem I.

2017-01-01

Fibrinogen and fibrin are essential for hemostasis and are major factors in thrombosis, wound healing, and several other biological functions and pathological conditions. The X-ray crystallographic structure of major parts of fibrin(ogen), together with computational reconstructions of missing portions and numerous biochemical and biophysical studies, have provided a wealth of data to interpret molecular mechanisms of fibrin formation, its organization, and properties. On cleavage of fibrinopeptides by thrombin, fibrinogen is converted to fibrin monomers, which interact via knobs exposed by fibrinopeptide removal in the central region, with holes always exposed at the ends of the molecules. The resulting half-staggered, double-stranded oligomers lengthen into protofibrils, which aggregate laterally to make fibers, which then branch to yield a three-dimensional network. Much is now known about the structural origins of clot mechanical properties, including changes in fiber orientation, stretching and buckling, and forced unfolding of molecular domains. Studies of congenital fibrinogen variants and post-translational modifications have increased our understanding of the structure and functions of fibrin(ogen). The fibrinolytic system, with the zymogen plasminogen binding to fibrin together with tissue-type plasminogen activator to promote activation to the active proteolytic enzyme, plasmin, results in digestion of fibrin at specific lysine residues. In spite of a great increase in our knowledge of all these interconnected processes, much about the molecular mechanisms of the biological functions of fibrin(ogen) remains unknown, including some basic aspects of clotting, fibrinolysis, and molecular origins of fibrin mechanical properties. Even less is known concerning more complex (patho)physiological implications of fibrinogen and fibrin. PMID:28101869

Topography and transport properties of oligo(phenylene ethynylene) molecular wires studied by scanning tunneling microscopy

NASA Technical Reports Server (NTRS)

Dholakia, Geetha R.; Fan, Wendy; Koehne, Jessica; Han, Jie; Meyyappan, M.

2003-01-01

Conjugated phenylene(ethynylene) molecular wires are of interest as potential candidates for molecular electronic devices. Scanning tunneling microscopic study of the topography and current-voltage (I-V) characteristics of self-assembled monolayers of two types of molecular wires are presented here. The study shows that the topography and I-Vs, for small scan voltages, of the two wires are quite similar and that the electronic and structural changes introduced by the substitution of an electronegative N atom in the central phenyl ring of these wires does not significantly alter the self-assembly or the transport properties.

Electric Field Tuning Molecular Packing and Electrical Properties of Solution-Shearing Coated Organic Semiconducting Thin Films

DOE PAGES

Molina-Lopez, Francisco; Yan, Hongping; Gu, Xiaodan; ...

2017-01-17

Recent improvements in solution-coated organic semiconductors (OSCs) evidence their high potential for cost-efficient organic electronics and sensors. Molecular packing structure determines the charge transport property of molecular solids. However, it remains challenging to control the molecular packing structure for a given OSC. Here, the application of alternating electric fields is reported to fine-tune the crystal packing of OSC solution-shearing coated at ambient conditions. First, a theoretical model based on dielectrophoresis is developed to guide the selection of the optimal conditions (frequency and amplitude) of the electric field applied through the solution-shearing blade during coating of OSC thin films. Next, electricmore » field-induced polymorphism is demonstrated for OSCs with both herringbone and 2D brick-wall packing motifs in 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene and 6,13-bis(triisopropylsilylethynyl) pentacene, respectively. Favorable molecular packing can be accessible in some cases, resulting in higher charge carrier mobilities. In conclusion, this work provides a new approach to tune the properties of solution-coated OSCs in functional devices for high-performance printed electronics.« less

Ambipolar carrier transport properties and molecular packing structure of octahexyl-substituted copper phthalocyanine

NASA Astrophysics Data System (ADS)

Watanabe, Ken; Watanabe, Koichi; Tohnai, Norimitsu; Itani, Hiromichi; Shimizu, Yo; Fujii, Akihiko; Ozaki, Masanori

2018-04-01

The charge carrier mobility of a solution-processable low-molecular-weight organic semiconductor material, i.e., 1,4,8,11,15,18,22,25-octahexylphthalocyanine copper complex (C6PcCu), was investigated by the time-of-flight technique. The anomalous ambipolar carrier mobility was discussed from the viewpoint of the molecular packing structure, which was clarified by single-crystal X-ray structure analysis. In the comparison between the molecular packing structures of C6PcCu and its metal-free-type homologue, it was found that the difference in carrier mobility originates from the rotation of the molecule, which is caused by the steric hindrance due to the introduction of a center metal and the interpenetration of the nonperipheral alkyl chains.

Anisotropy induced Kondo splitting in a mechanically stretched molecular junction: A first-principles based study

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

Wang, Xiaoli; Hou, Dong, E-mail: houdong@ustc.edu.cn; Zheng, Xiao, E-mail: xz58@ustc.edu.cn

2016-01-21

The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy–SH){sub 2} sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It ismore » confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.« less

Macro and micro analysis of small molecule diffusion in amorphous polymers

NASA Astrophysics Data System (ADS)

Putta, Santosh Krishna

In this study, both macroscopic and microscopic numerical techniques have been explored, to model and understand the diffusion behavior of small molecules in amorphous polymers, which very often do not follow the classical Fickian law. It was attempted to understand the influence of various aspects of the molecular structure of a polymer on its macroscopic diffusion behavior. At the macroscopic level, a hybrid finite-element/finite-difference model is developed to implement the coupled diffusion and deformation constitutive equations. A viscoelasticity theory, combined with time-freevolume superposition is used to model the deformation processes. A freevolume-based model is used to model the diffusion processes. The freevolume in the polymer is used as a coupling factor between the deformation and the diffusion processes. The model is shown to qualitatively describe some of the typical non-Fickian diffusion behavior in polymers. However, it does not directly involve the microstructure of a polymer. Further, some of the input parameters to the model are difficult to obtain experimentally. A numerical microscopic approach is therefore adopted to study the molecular structure of polymers. A molecular mechanics and dynamics technique combined with a modified Rotational Isomeric State (RIS) approach, is followed to generate the molecular structure for two types of polycarbonates, and, two types of polyacrylates, starting only with their chemical structures. A new efficient 3-D algorithm for Delaunay Tessellation is developed, and, then applied to discretize the molecular structure into Delaunay Tetrahedra. By using the dicretized molecular structure, size, shape, and, connectivity of free-spaces for small molecule diffusion in the above mentioned polymers, are then studied in relation to their diffusion properties. The influence of polymer and side chain flexibility, and diffusant-diffusant and diffusant-polymer molecular interactions, is also discussed with respect to the diffusion properties.

Applications of molecular modeling in coal research

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

Carlson, G.A.; Faulon, J.L.

Over the past several years, molecular modeling has been applied to study various characteristics of coal molecular structures. Powerful workstations coupled with molecular force-field-based software packages have been used to study coal and coal-related molecules. Early work involved determination of the minimum-energy three-dimensional conformations of various published coal structures (Given, Wiser, Solomon and Shinn), and the dominant role of van der Waals and hydrogen bonding forces in defining the energy-minimized structures. These studies have been extended to explore various physical properties of coal structures, including density, microporosity, surface area, and fractal dimension. Other studies have related structural characteristics to cross-linkmore » density and have explored small molecule interactions with coal. Finally, recent studies using a structural elucidation (molecular builder) technique have constructed statistically diverse coal structures based on quantitative and qualitative data on coal and its decomposition products. This technique is also being applied to study coalification processes based on postulated coalification chemistry.« less

Molecular structure of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-02-20

Quinoa starch has very small granules with unique properties. However, the molecular structure of quinoa starch remains largely unknown. In this study, composition and amylopectin molecular structure of 9 quinoa starch samples were characterised by chromatographic techniques. In particular, the amylopectin internal molecular structure, represented by φ, β-limit dextrins (LDs), was explored. Great variations in the composition and molecular structures were recorded among samples. Compared with other amylopectins, quinoa amylopectin showed a high ratio of short chain to long chains (mean:14.6) and a high percentage of fingerprint A-chains (A fp ) (mean:10.4%). The average chain length, external chain length, and internal chain length of quinoa amylopectin were 16.6, 10.6, and 5.00 glucosyl residues, respectively. Pearson correlation and principal component analysis revealed some inherent correlations among structural parameters and a similarity of different samples. Overall, quinoa amylopectins are structurally similar to that from starches with A-type polymorph such as oat and amaranth starches. Copyright © 2016 Elsevier Ltd. All rights reserved.

Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.

PubMed

Calhoun, Jennifer R; Liu, Weixia; Spiegel, Katrin; Dal Peraro, Matteo; Klein, Michael L; Valentine, Kathleen G; Wand, A Joshua; DeGrado, William F

2008-02-01

We report the solution NMR structure of a designed dimetal-binding protein, di-Zn(II) DFsc, along with a secondary refinement step employing molecular dynamics techniques. Calculation of the initial NMR structural ensemble by standard methods led to distortions in the metal-ligand geometries at the active site. Unrestrained molecular dynamics using a nonbonded force field for the metal shell, followed by quantum mechanical/molecular mechanical dynamics of DFsc, were used to relax local frustrations at the dimetal site that were apparent in the initial NMR structure and provide a more realistic description of the structure. The MD model is consistent with NMR restraints, and in good agreement with the structural and functional properties expected for DF proteins. This work demonstrates that NMR structures of metalloproteins can be further refined using classical and first-principles molecular dynamics methods in the presence of explicit solvent to provide otherwise unavailable insight into the geometry of the metal center.

Aggregate nanostructures of organic molecular materials.

PubMed

Liu, Huibiao; Xu, Jialiang; Li, Yongjun; Li, Yuliang

2010-12-21

Conjugated organic molecules are interesting materials because of their structures and their electronic, electrical, magnetic, optical, biological, and chemical properties. However, researchers continue to face great challenges in the construction of well-defined organic compounds that aggregate into larger molecular materials such as nanowires, tubes, rods, particles, walls, films, and other structural arrays. Such nanoscale materials could serve as direct device components. In this Account, we describe our recent progress in the construction of nanostructures formed through the aggregation of organic conjugated molecules and in the investigation of the optical, electrical, and electronic properties that depend on the size or morphology of these nanostructures. We have designed and synthesized functional conjugated organic molecules with structural features that favor assembly into aggregate nanostructures via weak intermolecular interactions. These large-area ordered molecular aggregate nanostructures are based on a variety of simpler structures such as fullerenes, perylenes, anthracenes, porphyrins, polydiacetylenes, and their derivatives. We have developed new methods to construct these larger structures including organic vapor-solid phase reaction, natural growth, association via self-polymerization and self-organization, and a combination of self-assembly and electrochemical growth. These methods are both facile and reliable, allowing us to produce ordered and aligned aggregate nanostructures, such as large-area arrays of nanowires, nanorods, and nanotubes. In addition, we can synthesize nanoscale materials with controlled properties. Large-area ordered aggregate nanostructures exhibit interesting electrical, optical, and optoelectronic properties. We also describe the preparation of large-area aggregate nanostructures of charge transfer (CT) complexes using an organic solid-phase reaction technique. By this process, we can finely control the morphologies and sizes of the organic nanostructures on wires, tubes, and rods. Through field emission studies, we demonstrate that the films made from arrays of CT complexes are a new kind of cathode materials, and we systematically investigate the effects of size and morphology on electrical properties. Low-dimension organic/inorganic hybrid nanostructures can be used to produce new classes of organic/inorganic solid materials with properties that are not observed in either the individual nanosize components or the larger bulk materials. We developed the combined self-assembly and templating technique to construct various nanostructured arrays of organic and inorganic semiconductors. The combination of hybrid aggregate nanostructures displays distinct optical and electrical properties compared with their individual components. Such hybrid structures show promise for applications in electronics, optics, photovoltaic cells, and biology. In this Account, we aim to provide an intuition for understanding the structure-function relationships in organic molecular materials. Such principles could lead to new design concepts for the development of new nonhazardous, high-performance molecular materials on aggregate nanostructures.

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial properties.

Amylopectin molecular structure in relation to physicochemical properties of quinoa starch.

PubMed

Li, Guantian; Zhu, Fan

2017-05-15

Structure-function relationships of starch components remain a subject of research interest. Quinoa starch has very small granules (∼2μm) with unique properties. In this study, nine quinoa starches varied greatly in composition, structure, and physicochemical properties were selected for the analysis of structure-function relationships. Pearson correlation analysis revealed that the properties related to gelatinization such as swelling power, water solubility index, crystallinity, pasting, and thermal properties are much affected by the amylopectin chain profile and amylose content. The parameters of gel texture and amylose leaching are much related to amylopectin internal structure. Other properties such as enzyme susceptibility and particle size distribution are also strongly correlated with starch composition and amylopectin structure. Interesting findings indicate the importance of amylopectin internal structure and individual unit chain profile in determining the physicochemical properties of starch. This work highlights some relationships among composition, amylopectin structure and physicochemical properties of quinoa starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

Thiophene-Based Organic Semiconductors.

PubMed

Turkoglu, Gulsen; Cinar, M Emin; Ozturk, Turan

2017-10-24

Thiophene-based π-conjugated organic small molecules and polymers are the research subject of significant current interest owing to their potential use as organic semiconductors in material chemistry. Despite simple and similar molecular structures, the hitherto reported properties of thiophene-based organic semiconductors are rather diverse. Design of high performance organic semiconducting materials requires a thorough understanding of inter- and intra-molecular interactions, solid-state packing, and the influence of both factors on the charge carrier transport. In this chapter, thiophene-based organic semiconductors, which are classified in terms of their chemical structures and their structure-property relationships, are addressed for the potential applications as organic photovoltaics (OPVs), organic field-effect transistors (OFETs) and organic light emitting diodes (OLEDs).

Molecular dynamics simulations to study the solvent influence on protein structure

NASA Astrophysics Data System (ADS)

Dominguez, Hector

2016-05-01

Molecular simulations were carried out to study the influence of different water models in two protein systems. Most of the solvents used in protein simulations, e.g., SPC/E or TIP3P, fail to reproduce the bulk water static dielectric constant. Recently a new water model, TIP4P/ɛ, which reproduces the experimental dielectric constant was reported. Therefore, simulations for two different proteins, Lysozyme and Ubiquitin with SPC/E, TIP3P and TIP4P/ɛ solvents were carried out. Dielectric constants and structural properties were calculated and comparisons were conducted. The structural properties between the three models are very similar, however, the dielectric constants are different in each case.

Uncovering the structure-function relationship in spider silk

NASA Astrophysics Data System (ADS)

Yarger, Jeffery L.; Cherry, Brian R.; van der Vaart, Arjan

2018-03-01

All spiders produce protein-based biopolymer fibres that we call silk. The most studied of these silks is spider dragline silk, which is very tough and relatively abundant compared with other types of spider silks. Considerable research has been devoted to understanding the relationship between the molecular structure and mechanical properties of spider dragline silks. In this Review, we overview experimental and computational studies that have provided a wealth of detail at the molecular level on the highly conserved repetitive core and terminal regions of spider dragline silk. We also discuss the role of the nanocrystalline β-sheets and amorphous regions in determining the properties of spider silk fibres, endowing them with strength and elasticity. Additionally, we outline imaging techniques and modelling studies that elucidate the importance of the hierarchical structure of silk fibres at the molecular level. These insights into structure-function relationships can guide the reverse engineering of spider silk to enable the production of superior synthetic fibres.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennite -- A Computational Modeling Study

NASA Astrophysics Data System (ADS)

Adebiyi, Babatunde Mattew

Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance, are required. A computational material modeling methodology is investigated and demonstrated for a key cement hydrated component material chemistry structure of Calcium-Silicate-Hydrate (C-S-H) Jennite in this work. The effect of material ion exchanges on the mechanical stiffness properties and shear deformation behavior of hydrated cement material chemistry structure of Calcium Silicate Hydrate (C-S-H) Jennite was studied. Calcium ions were replaced with Magnesium ions in Jennite structure of the C-S-H gel. Different level of substitution of the ions was used. The traditional Jennite structure was obtained from the American Mineralogist Crystal Structure Database and super cells of the structures were created using a Molecular Dynamics Analyzer and Visualizer Material Studio. Molecular dynamics parameters used in the modeling analysis were determined by carrying out initial dynamic studies. 64 unit cell of C-S-H Jennite was used in material modeling analysis studies based on convergence results obtained from the elastic modulus and total energies. NVT forcite dynamics using COMPASS force field based on 200 ps dynamics time was used to determine mechanical modulus of the traditional C-S-H gel and the Magnesium ion modified structures. NVT Discover dynamics using COMPASS forcefield was used in the material modeling studies to investigate the influence of ionic exchange on the shear deformation of the associated material chemistry structures. A prior established quasi-static deformation method to emulate shear deformation of C-S-H material chemistry structure that is based on a triclinic crystal structure was used, by deforming the triclinic crystal structure at 0.2 degree per time step for 75 steps of deformation. It was observed that there is a decrease in the total energies of the systems as the percentage of magnesium ion increases in the C-S-H Jennite molecular structure systems. Investigation of effect of ion exchange on the elastic modulus shows that the elastic stiffness modulus tends to decrease as the amount of Mg in the systems increases, using either COMPASS or universal force field. On the other hand, shear moduli obtained after deforming the structures computed from the stress-strain curve obtained from material modeling increases as the amount of Mg increases in the system. The present investigations also showed that ultimate shear stress obtained from predicted shear stress---strain also increases with amount of Mg in the chemistry structure. Present study clearly demonstrates that computational material modeling following molecular dynamics analysis methodology is an effective way to predict and understand the effective material chemistry and additive changes on the stiffness and deformation characteristics in cementitious materials, and the results suggest that this method can be extended to other materials.

Predicting the Highly Nonlinear Mechanical Properties of Polymeric Materials

NASA Astrophysics Data System (ADS)

Porter, David

2009-06-01

Over the past few years, we have developed models that calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular and morphological structure. A review of these models is presented here, with emphasis on combining the fundamental aspects of molecular physics that dictate these properties and the pragmatic need to make realistic predictions for our customers; the designer of new materials and the engineers who use these materials. The models calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular structure. The model is based upon the premise that mechanical properties are a direct consequence of energy stored and energy dissipated during deformation of a material. This premise is transformed into a consistent set of structure-property relations for the equation of state, EoS, and the engineering constitutive relations in a polymer by quantifying energy storage and loss at the molecular level of interactions between characteristic groups of atoms in a polymer. These relations are derived from a simple volumetric mean field Lennard-Jones potential function for the potential energy of intermolecular interactions in a polymer. First, properties such as temperature-volume relations and glass transition temperature are calculated directly from the potential function. Then, the `shock' EoS is derived simply by differentiating the potential function with respect to volume, assuming that the molecules cannot relax in the time scales of the deformation. The energy components are then used to predict the dynamic mechanical spectrum of a polymer in terms of temperature and rate. This can be transformed directly into the highly nonlinear stress-strain relations through yield. The constitutive relations are formulated as a set of analytical equations that predict properties directly in terms of a small set of structural parameters that can be calculated directly and independently from the chemical composition and morphology of a polymer. A number of examples are given to illustrate the model and also to show that the method can be applied, with appropriate modifications, to other materials.

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Synthesis, structural characterization and comparison of experimental and theoretical results by DFT level of molecular structure of 4-(4-methoxyphenethyl)-3,5-dimethyl-4H-1,2,4-triazole.

PubMed

Düğdü, Esra; Ünver, Yasemin; Ünlüer, Dilek; Tanak, Hasan; Sancak, Kemal; Köysal, Yavuz; Işık, Şamil

2013-05-01

4-(4-Methoxyphenethyl)-3,5-dimethyl-4H-1,2,4-triazole (3) was synthesized from the reaction of ethyl N'-acetylacetohydrazonate (1) with 2-(4-methoxyphenyl)ethanamine (2). The structure of the title compound 3 has been inferred through IR, (1)H/(13)C NMR, mass spectrometry, elemental analyses and combination of X-ray crystallography and theoretical methods. In addition to the molecular geometry from X-ray determination, the molecular geometry and vibrational frequencies of the title compound 3 in the ground state, were calculated using the density functional method (B3LYP) with the 6-31G(d) basis set. The calculated results show that the optimized geometry can well reproduce the crystal structure and the theoretical vibrational frequencies show good agreement with experimental values. The nonlinear optical properties are also addressed theoretically. The predicted nonlinear optical properties of 3 are greater than ones of urea. In addition, DFT calculations of molecular electrostatic potentials and frontier molecular orbitals of the title compound were carried out at the B3LYP/6-31G(d) level of theory. Copyright © 2012. Published by Elsevier B.V.

Toward the identification of molecular cogs.

PubMed

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.

Non-linear optical techniques and optical properties of condensed molecular systems

NASA Astrophysics Data System (ADS)

Citroni, Margherita

2013-06-01

Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.

Transforming Benzophenoxazine Laser Dyes into Chromophores for Dye-Sensitized Solar Cells: A Molecular Engineering Approach

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

Schröder, Florian A. Y. N.; Cole, Jacqueline M.; Waddell, Paul G.

2015-02-03

The re-functionalization of a series of four well-known industrial laser dyes, based on benzophenoxazine, is explored with the prospect of molecularly engineering new chromophores for dye-sensitized solar cell (DSC) applications. Such engineering is important since a lack of suitable dyes is stifling the progress of DSC technology. The conceptual idea involves making laser dyes DSC-active by chemical modification, while maintaining their key property attributes that are attractive to DSC applications. This molecular engineering follows a step-wise approach. Firstly, molecular structures and optical absorption properties are determined for the parent laser dyes: Cresyl Violet (1); Oxazine 170 (2); Nile Blue Amore » (3), Oxazine 750 (4). These reveal structure-property relationships which define the prerequisites for computational molecular design of DSC dyes; the nature of their molecular architecture (D-π-A) and intramolecular charge transfer. Secondly, new DSC dyes are computationally designed by the in silico addition of a carboxylic acid anchor at various chemical substitution points in the parent laser dyes. A comparison of the resulting frontier molecular orbital energy levels with the conduction band edge of a TiO2 DSC photoanode and the redox potential of two electrolyte options I-/I3- and Co(II/III)tris(bipyridyl) suggests promise for these computationally designed dyes as co-sensitizers for DSC applications.« less

Theoretical Studies for Dendrimer-Based Drug Delivery.

PubMed

Bello, Martiniano; Fragoso-Vázquez, Jonathan; Correa-Basurto, José

2017-01-01

Numerous theoretical studies have been performed to iteratively optimize the physicochemical properties such as dendrimer size and surface constituents in solution, as well as their molecular recognition properties for drugs, lipid membranes, nucleic acids and proteins, etc. Molecular modeling approaches such as docking and molecular dynamic (MD) simulations have supported experimental efforts by providing important insights into the structural properties of dendrimers in solution and possible binding properties of drugs at the atomic level. We review the utilization of molecular modelling tools to obtain insight into the study and design of dendrimers, with particular importance placed on the improvement of binding properties of dendrimers for their use as drug nanocarriers and to increase the water solubility properties and drug delivery. The modeling studies discussed in this review have provided substantial insight into the physicochemical properties of dendrimers in solution, including solvent pH and counterion distribution, at the atomic level, as well as the elucidation of some of the key interactions in solution of unmodified and modified dendrimers with some drugs of pharmaceutics interest and biological systems such as nucleic acids, proteins and lipid membranes. the described studies illustrate that whether simulations will be run at the all-atom or coarse-grained level, physicochemical conditions such as the type of force field, the treatment of electrostatics effects, counterion distribution, protonation state of dendrimers, and dendrimer concentrations which have been probed to play a crucial role in the structural behavior and binding properties must be prudently incorporated in the simulations. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Lattice thermal conductivity of monolayer AsP from first-principles molecular dynamics.

PubMed

Sun, Yajing; Shuai, Zhigang; Wang, Dong

2018-05-23

Few-layered arsenic-phosphorus alloys, AsxP(1-x), with a puckered structure have been recently synthesized and demonstrated with fully tunable band gaps and optical properties. It is predicted that the carrier mobility of monolayer AsP compounds is even higher than that of black phosphorene (b-P). The anisotropic and orthogonal electrical and thermal transport properties of the puckered group VA elements make them intriguing materials for thermoelectric applications. Herein, we investigated the thermal transport properties of AsP based on first-principles molecular dynamics and the Boltzmann transport equation. We reveal that monolayer AsP with three different chemical structures possesses thermal conductivities lower than b-P, but with increased anisotropy. Further, these structures behave profoundly different on heat conduction. This can be attributed to the distinct low-frequency optical modes associated with their bonding nature. Our results highlight the impact of atomic arrangement on the thermal conductivity of AsP, and the structure-property relationship established may guide the fabrication of thermoelectric materials via the engineered alloying method.

Influence of C-H···O Hydrogen Bonds on Macroscopic Properties of Supramolecular Assembly.

PubMed

Ji, Wei; Liu, Guofeng; Li, Zijian; Feng, Chuanliang

2016-03-02

For CH···O hydrogen bonds in assembled structures and the applications, one of the critical issues is how molecular spatial structures affect their interaction modes as well as how to translate the different modes into the macroscopic properties of materials. Herein, coumarin-derived isomeric hydrogelators with different spatial structures are synthesized, where only nitrogen atoms locate at the ortho, meso, or para position in the pyridine ring. The gelators can self-assemble into single crystals and nanofibrous networks through CH···O interactions, which are greatly influenced by nitrogen spatial positions in the pyridine ring, leading to the different self-assembly mechanisms, packing modes, and properties of the nanofibrous networks. Typically, different cell proliferation rates are obtained on the different CH···O bonds driving nanofibrous structures, implying that tiny variation of the stereo-position of nitrogen atoms can be sensitively detected by cells. The study paves a novel way to investigate the influence of isomeric molecular assembly on macroscopic properties and functions of materials.

How Water’s Properties Are Encoded in Its Molecular Structure and Energies

PubMed Central

2017-01-01

How are water’s material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth’s living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies—water’s solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions—hydroxide and protons—diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water’s molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water’s orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties. PMID:28949513

Modelling of Molecular Structures and Properties. Proceedings of the International Meeting of Physical Chemistry on Modeling of Molecular Structures and Properties in Physical Chemistry and Biophysics Organized by the Division de Chimie Physique of the Societe Francaise de Chimie Held in Nancy, France on 11-15 September 1989

DTIC Science & Technology

1990-01-01

expert systems, "intelligent" computer-aided instruction , symbolic learning . These aspects will be discussed, focusing on the specific problems the...VLSI chips) according to preliminary specifications. Finally ES are also used in computer-aided instruction (CAI) due to their ability of... instructions to process controllers), academic teaching (for mathematics , physics, foreign language, etc.). Domains of application The different

Recognition of the folded conformation of plant hormone (auxin, IAA) conjugates with glutamic and aspartic acids and their amides

NASA Astrophysics Data System (ADS)

Antolić, S.; Kveder, M.; Klaić, B.; Magnus, V.; Kojić-Prodić, B.

2001-01-01

The molecular structure of the endogenous plant hormone (auxin) conjugate, N-(indol-3-ylacetyl)-L-glutamic acid, is deduced by comparison with N2-(indol-3-ylacetyl)glutamine (IAA-Gln), N2-(indol-3-ylacetyl)asparagine (IAA-Asn) and N-(indol-3-ylacetyl)-L-aspartic acid using X-ray structure analysis, 1H-NMR spectroscopy (NOE measurements) and molecular modelling. The significance of the overall molecular shape, and of the resulting amphiphilic properties, of the compounds studied are discussed in terms of possible implications for trafficking between cell compartments. Both in the solid state and in solution, the molecules are in the hair-pin (folded) conformation in which the side chain is folded over the indole ring. While extended conformations can be detected by molecular dynamics simulations, they are so short-lived that any major influence on the biological properties of the compounds studied is unlikely.

Molecular engineering of antibodies for therapeutic and diagnostic purposes

PubMed Central

Ducancel, Frédéric; Muller, Bruno H.

2012-01-01

During the past ten years, monoclonal antibodies (mAbs) have taken center stage in the field of targeted therapy and diagnosis. This increased interest in mAbs is due to their binding accuracy (affinity and specificity) together with the original molecular and structural rules that govern interactions with their cognate antigen. In addition, the effector properties of antibodies constitute a second major advantage associated with their clinical use. The development of molecular and structural engineering and more recently of in vitro evolution of antibodies has opened up new perspectives in the de novo design of antibodies more adapted to clinical and diagnostic use. Thus, efforts are regularly made by researchers to improve or modulate antibody recognition properties, to adapt their pharmacokinetics, engineer their stability, and control their immunogenicity. This review presents the latest molecular engineering results on mAbs with therapeutic and diagnostic applications. PMID:22684311

Molecular Cloud Structures and Massive Star Formation in N159

NASA Astrophysics Data System (ADS)

Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

2018-02-01

The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.

Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

NASA Astrophysics Data System (ADS)

Chen, Kai; Leong, Eunice Sok Ping; Rukavina, Michael; Nagao, Tadaaki; Liu, Yan Jun; Zheng, Yuebing

2015-06-01

Molecular plasmonics explores and exploits the molecule-plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP). Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional) of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.

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

Structural properties of CuAu nanoparticles with different type. Molecular dynamic simulations

NASA Astrophysics Data System (ADS)

Chepkasov, I. V.; Baidyshev, V. S.; Baev, A. Y.

2018-05-01

The paper is devoted to the thermal stability of a CuAu nanoparticles structure (D=5 nm) of various type (binary alloy, core-shell, "Janus" type) and of various percentage of copper atoms. The simulation was carried out with molecular dynamics, using the embedded atom potential. The authors defined the most preferable structural options from the standpoint of thermodynamics, as well as studied in detail the influence of different temperatures on the structural stability of CuAu nanoparticles.

Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

PubMed

Schwaben, Jonas; Münster, Niels; Klues, Michael; Breuer, Tobias; Hofmann, Philipp; Harms, Klaus; Witte, Gregor; Koert, Ulrich

2015-09-21

Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biochemical and functional characterization of an albumin protein belonging to the hemopexin superfamily from Lens culinaris seeds.

PubMed

Scarafoni, Alessio; Gualtieri, Elisa; Barbiroli, Alberto; Carpen, Aristodemo; Negri, Armando; Duranti, Marcello

2011-09-14

The present paper reports the purification and biochemical characterization of an albumin identified in mature lentil seeds with high sequence similarity to pea PA2. These proteins are found in many edible seeds and are considered potentially detrimental for human health due to the potential allergenicity and lectin-like activity. Thus, the description of their possible presence in food and the assessment of the molecular properties are relevant. The M(r), pI, and N-terminal sequence of this protein have been determined. The work included the study of (i) the binding properties to hemine to assess the presence of hemopexin structural domains and (ii) the binding properties of the protein to thiamin. In addition, the structural changes induced by heating have been evaluated by means of spectroscopic techniques. Denaturation temperature has also been determined. The present work provides new insights about the structural molecular features and the ligand-binding properties and dynamics of this kind of seed albumin.

Structure-Property Relationships of Organic Electrolytes and Their Effects on Li/S Battery Performance.

PubMed

Kaiser, Mohammad Rejaul; Chou, Shulei; Liu, Hua-Kun; Dou, Shi-Xue; Wang, Chunsheng; Wang, Jiazhao

2017-12-01

Electrolytes, which are a key component in electrochemical devices, transport ions between the sulfur/carbon composite cathode and the lithium anode in lithium-sulfur batteries (LSBs). The performance of a LSB mostly depends on the electrolyte due to the dissolution of polysulfides into the electrolyte, along with the formation of a solid-electrolyte interphase. The selection of the electrolyte and its functionality during charging and discharging is intricate and involves multiple reactions and processes. The selection of the proper electrolyte, including solvents and salts, for LSBs strongly depends on its physical and chemical properties, which is heavily controlled by its molecular structure. In this review, the fundamental properties of organic electrolytes for LSBs are presented, and an attempt is made to determine the relationship between the molecular structure and the properties of common organic electrolytes, along with their effects on the LSB performance. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular design for enhancement of ocular penetration.

PubMed

Shirasaki, Yoshihisa

2008-07-01

Over the past two decades, many oral drugs have been designed in consideration of physicochemical properties to attain optimal pharmacokinetic properties. This strategy significantly reduced attrition in drug development owing to inadequate pharmacokinetics during the last decade. On the other hand, most ophthalmic drugs are generated from reformulation of other therapeutic dosage forms. Therefore, the modification of formulations has been used mainly as the approach to improve ocular pharmacokinetics. However, to maximize ocular pharmacokinetic properties, a specific molecular design for ocular drug is preferable. Passive diffusion of drugs across the cornea membranes requires appropriate lipophilicity and aqueous solubility. Improvement of such physicochemical properties has been achieved by structure optimization or prodrug approaches. This review discusses the current knowledge about ophthalmic drugs adapted from systemic drugs and molecular design for ocular drugs. I propose the approaches for molecular design to obtain the optimal ocular penetration into anterior segment based on published studies to date.

Theoretical studies on the electronic structure and spectroscopic properties of transition metals bis(dipyrrinate)s

NASA Astrophysics Data System (ADS)

Ksenofontov, Alexander A.; Guseva, Galina B.; Antina, Elena V.

2016-10-01

Density functional theory (DFT) and Time-dependent density functional theory (TD- DFT) computations have been used to reveal structural, molecular, electronic and spectral-luminescent parameters and features of several homoleptic transition metals bis(dipyrrine) complexes. The influence of complexing agent and ligand nature on the regularities in geometric, spectral-luminescent properties, kinetic and thermal stability changes in the [M2L2] complexes series were studied. Special attention is paid to the influence of the solvating media (PCM/TD-B3LYP/Def2-SVP) on changing spectral-luminescent properties of d-metals bis(dipyrrinate)s. The interpretation of the dependence between spectral-luminescent properties of the complexes and HOMO-LUMO (highest occupied molecular orbital and lowest unoccupied molecular orbital) energy gap's width was given. It was shown that the regularities in changing the helicates' quantum yield depending on the nature of complexing agent, ligand and solvent properties, obtained from quantum-chemical calculations, are in the agreement with our previously obtained experimental data. Thus, structural and spectral-luminescent characteristics of new [M2L2] luminophors can be evaluated with high reliability, and good forecast prospects for their use as fluorescent dyes for optical devices can be made in terms of the results of theoretical studies (B3LYP/Def2-SVP and TD-B3LYP/Def2-SVP).

Robust optical properties of sandwiched lateral composition modulation GaInP structure grown by molecular beam epitaxy

DOE PAGES

Park, Kwangwook; Kang, Seokjin; Ravindran, Sooraj; ...

2016-12-26

Double-hetero structure lateral composition modulated (LCM) GaInP and sandwiched LCM GaInP having the same active layer thickness were grown and their optical properties were compared. Sandwiched LCM GaInP showed robust optical properties due to periodic potential nature of the LCM structure, and the periodicity was undistorted even for thickness far beyond the critical layer thickness. A thick LCM GaInP structure with undistorted potential that could preserve the properties of native LCM structure was possible by stacking thin LCM GaInP structures interspaced with strain compensating GaInP layers. Furthermore, the sandwiched structure could be beneficial in realizing the LCM structure embedded highmore » efficiency solar cells.« less

Electrical conduction in polymer dielectrics

NASA Technical Reports Server (NTRS)

Cotts, D. B.

1985-01-01

The use of polymer dielectrics with moderate resistivities could reduce or eliminate problems associated with spacecraft charging. The processes responsible for conduction and the properties of electroactive polymers are reviewed, and correlations drawn between molecular structure and electrical conductivity. These structure-property relationships led to the development of several new electroactive polymer compositions and the identification of several systems that have the requisite thermal, mechanical, environmental and electrical properties for use in spacecraft.

Molecular modeling of the microstructure evolution during carbon fiber processing

NASA Astrophysics Data System (ADS)

Desai, Saaketh; Li, Chunyu; Shen, Tongtong; Strachan, Alejandro

2017-12-01

The rational design of carbon fibers with desired properties requires quantitative relationships between the processing conditions, microstructure, and resulting properties. We developed a molecular model that combines kinetic Monte Carlo and molecular dynamics techniques to predict the microstructure evolution during the processes of carbonization and graphitization of polyacrylonitrile (PAN)-based carbon fibers. The model accurately predicts the cross-sectional microstructure of the fibers with the molecular structure of the stabilized PAN fibers and physics-based chemical reaction rates as the only inputs. The resulting structures exhibit key features observed in electron microcopy studies such as curved graphitic sheets and hairpin structures. In addition, computed X-ray diffraction patterns are in good agreement with experiments. We predict the transverse moduli of the resulting fibers between 1 GPa and 5 GPa, in good agreement with experimental results for high modulus fibers and slightly lower than those of high-strength fibers. The transverse modulus is governed by sliding between graphitic sheets, and the relatively low value for the predicted microstructures can be attributed to their perfect longitudinal texture. Finally, the simulations provide insight into the relationships between chemical kinetics and the final microstructure; we observe that high reaction rates result in porous structures with lower moduli.

Confinement properties of 2D porous molecular networks on metal surfaces

NASA Astrophysics Data System (ADS)

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-04-01

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

Confinement properties of 2D porous molecular networks on metal surfaces.

PubMed

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-04-20

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

Nanogap structures for molecular nanoelectronics.

PubMed

Motto, Paolo; Dimonte, Alice; Rattalino, Ismael; Demarchi, Danilo; Piccinini, Gianluca; Civera, Pierluigi

2012-02-09

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes.

Synthesis, spectroscopic characterization and crystallographic behavior of a biologically relevant novel indole-fused heterocyclic compound - Experimental and theoretical (DFT) studies

NASA Astrophysics Data System (ADS)

Sharma, Sakshi; Brahmachari, Goutam; Banerjee, Bubun; Nurjamal, Khondekar; Kumar, Abhishek; Srivastava, Ambrish Kumar; Misra, Neeraj; Pandey, Sarvesh Kumar; Rajnikant; Gupta, Vivek K.

2016-08-01

The present communication deals with the eco-friendly synthesis, spectral properties and X-ray crystal structure of an indole derivative - Ethyl 2'-amino-3'-cyano-6'-methyl-5-nitro-2-oxospiro [indoline-3,4'-pyran]-5'-carboxylate. The title compound was synthesized in 87% yield. The crystal structure of the molecule is stabilized by intermolecular Nsbnd H … N, Nsbnd H … O and Csbnd H … π interactions. The molecule is organized in the crystal lattice forming sheet like structure. To interpret the experimental data, ab initio computations of the vibrational frequencies were carried out using the Gaussian 09 program followed by the full optimizations done using Density Functional Theory (DFT) at B3LYP/6-31 + G(d,p) level. The combined use of experiments and computations allowed a firm assignment of the majority of observed bands for the compound. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap were presented. The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs) and density of states (DOS). From the optimized geometry of the molecule, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title compound have been calculated in the ground state theoretically. The theoretical results showed good agreement with the experimental values. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compound.

Molecularly thin fluoro-polymeric nanolubricant films: tribology, rheology, morphology, and applications.

PubMed

Chung, Pil Seung; Jhon, Myung S; Choi, Hyoung Jin

2016-03-21

Molecularly thin perfluoropolyether (PFPE) has been used extensively as a high-performance lubricant in various applications and, more importantly, on carbon overcoats to enhance the reliability and lubrication of micro-/nanoelectro-mechanical systems, where the tribological performance caused by its molecular architecture is a critical issue, as are its physical properties and rheological characteristics. This Highlight addresses recent trends in the development of fluoro-polymeric lubricant films with regard to their tribology, rheology, and physio-chemical properties as they relate to heat-assisted magnetic recording. Nanorheology has been employed to examine the dynamic response of nonfunctional and functional PFPEs, while the viscoelastic properties of nanoscale PFPE films and the relaxation processes as a function of molecular structure and end-group functionality were analyzed experimentally; furthermore, the characteristics of binary blends were reported.

Self-organizing layers from complex molecular anions

DOE PAGES

Warneke, Jonas; McBriarty, Martin E.; Riechers, Shawn L.; ...

2018-05-14

The formation of traditional ionic materials occurs principally via joint accumulation of both anions and cations. Here in this paper, we describe a previously unreported phenomenon by which macroscopic liquid-like thin layers with tunable self-organization properties form through accumulation of stable complex ions of one polarity on surfaces. Using a series of highly stable molecular anions we demonstrate a strong influence of the internal charge distribution of the molecular ions, which is usually shielded by counterions, on the properties of the layers. Detailed characterization reveals that the intrinsically unstable layers of anions on surfaces are stabilized by simultaneous accumulation ofmore » neutral molecules from the background environment. Different phases, self-organization mechanisms and optical properties are observed depending on the molecular properties of the deposited anions, the underlying surface and the coadsorbed neutral molecules. This demonstrates rational control of the macroscopic properties (morphology and size of the formed structures) of the newly discovered anion-based layers.« less

Self-organizing layers from complex molecular anions

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

Warneke, Jonas; McBriarty, Martin E.; Riechers, Shawn L.

The formation of traditional ionic materials occurs principally via joint accumulation of both anions and cations. Here in this paper, we describe a previously unreported phenomenon by which macroscopic liquid-like thin layers with tunable self-organization properties form through accumulation of stable complex ions of one polarity on surfaces. Using a series of highly stable molecular anions we demonstrate a strong influence of the internal charge distribution of the molecular ions, which is usually shielded by counterions, on the properties of the layers. Detailed characterization reveals that the intrinsically unstable layers of anions on surfaces are stabilized by simultaneous accumulation ofmore » neutral molecules from the background environment. Different phases, self-organization mechanisms and optical properties are observed depending on the molecular properties of the deposited anions, the underlying surface and the coadsorbed neutral molecules. This demonstrates rational control of the macroscopic properties (morphology and size of the formed structures) of the newly discovered anion-based layers.« less

Molecular dynamics simulation of thermomechanical properties of montmorillonite crystal. 1. Isolated clay nanoplate.

PubMed

Mazo, Mikhail A; Manevitch, Leonid I; Gusarova, Elena B; Shamaev, Mikhail Yu; Berlin, Alexander A; Balabaev, Nikolay K; Rutledge, Gregory C

2008-03-13

The structure and mechanical properties of clay nanoparticles is a subject of growing interest because of their numerous applications in engineering. We present the results of molecular dynamics simulation for a single nanoplate of pyrophyllite - a 2:1 clay mineral consisting of two tetrahedral sheets of SiO4 and an intervening octahedral AlO6 sheet. Simulations were performed in the temperature interval from 5 to 750 K using the ionic-type potentials of Cygan et al. On this basis the temperature dependences of structural parameters, characterizing both tetrahedral and octahedral sheets as well as single lamella, have been studied. Two slightly different structures were observed in this wide temperature interval. The mechanical properties of the nanoplate were calculated from stress-strain diagrams, which have been obtained at relatively slow rates of deformation (for molecular simulations). Using different types of loading, we calculated the full elasticity tensor and estimated the influence of temperature on its components. We estimated also the bending and torsion stiffnesses of the nanoplate as specific characteristics of this type of particle. Because the nanoplate is atomically thin, a reasonable determination of the thickness is a nontrivial problem, both in the modeling of mechanical properties and in physical interpretation of the obtained data. We propose a procedure for its calculation.

DFT Studies of Graphene-Functionalised Derivatives of Capecitabine

NASA Astrophysics Data System (ADS)

Aramideh, Mehdi; Mirzaei, Mahmoud; Khodarahmi, Ghadamali; Gülseren, Oğuz

2017-11-01

Cancer is one of the major problems for so many people around the world; therefore, dedicating efforts to explore efficient therapeutic methodologies is very important for researchers of life sciences. In this case, nanostructures are expected to be carriers of medicinal compounds for targeted drug design and delivery purposes. Within this work, the graphene (Gr)-functionalised derivatives of capecitabine (CAP), as a representative anticancer, have been studied based on density functional theory calculations. Two different sizes of Gr molecular models have been used for the functionalisation of CAP counterparts, CAP-Gr3 and CAP-Gr5, to explore the effects of Gr-functionalisation on the original properties of CAP. All singular and functionalised molecular models have been optimised and the molecular and atomic scale properties have been evaluated for the optimised structures. Higher formation favourability has been obtained for CAP-Gr5 in comparison with CAP-Gr3 and better structural stability has been obtained in the water-solvated system than the isolated gas-phase system for all models. The CAP-Gr5 model could play a better role of electron transferring in comparison with the CAP-Gr3 model. As a concluding remark, the molecular properties of CAP changed from singular to functionalised models whereas the atomic properties remained almost unchanged, which is expected for a carrier not to use significant perturbations to the original properties of the carried counterpart.

The Eyes Have It: A Problem-Based Learning Exercise in Molecular Evolution

ERIC Educational Resources Information Center

White, Harold B.

2007-01-01

Molecular evolution provides an interesting context in which to use problem-based learning because it integrates a variety of topics in biology, biochemistry, and molecular biology. This three-stage problem for advanced students deals with the structure, multiple functions, and properties of lactate dehydrogenase isozymes, and the related…

A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

ERIC Educational Resources Information Center

Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

2011-01-01

Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

Structure-function-property-design interplay in biopolymers: spider silk.

PubMed

Tokareva, Olena; Jacobsen, Matthew; Buehler, Markus; Wong, Joyce; Kaplan, David L

2014-04-01

Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure-function-property relationships. The relationships between molecular composition, secondary structures and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

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

Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

PubMed

Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

2016-11-15

Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic errors in the enthalpy and entropy cancel somewhat. Second, because solid state nuclear magnetic resonance (NMR) plays an increasingly important role in molecular crystal studies, this Account discusses how fragment methods can be used to achieve higher-accuracy chemical shifts in molecular crystals. Whereas widely used plane wave density functional theory models are largely restricted to generalized gradient approximation (GGA) functionals like PBE in practice, fragment methods allow the routine use of hybrid density functionals with only modest increases in computational cost. In extensive molecular crystal benchmarks, hybrid functionals like PBE0 predict chemical shifts with 20-30% higher accuracy than GGAs, particularly for 1 H, 13 C, and 15 N nuclei. Due to their higher sensitivity to polarization effects, 17 O chemical shifts prove slightly harder to predict with fragment methods. Nevertheless, the fragment model results are still competitive with those from GIPAW. The improved accuracy achievable with fragment approaches and hybrid density functionals increases discrimination between different potential assignments of individual shifts or crystal structures, which is critical in NMR crystallography applications. This higher accuracy and greater discrimination are highlighted in application to the solid state NMR of different acetaminophen and testosterone crystal forms.

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

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

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

Self-Assembly of Alkylammonium Chains on Montmorillonite: Effect of Interlayer Cations, CEC, and Chain Length

NASA Astrophysics Data System (ADS)

Chen, Hua; Li, Yingjun; Zhou, Yuanlin; Wang, Shanqiang; Zheng, Jian; He, Jiacai

2017-12-01

Recently, polymeric materials have been filled with synthetic or natural inorganic compounds in order to improve their properties. Especially, polymer clay nanocomposites have attracted both academic and industrial attention. Currently, the structure and physical phenomena of organoclays at molecular level are difficultly explained by existing experimental techniques. In this work, molecular dynamics (MD) simulation was executed using the CLAYFF and CHARMM force fields to evaluate the structural properties of organoclay such as basal spacing, interlayer density, energy and the arrangement of alkyl chains in the interlayer spacing. Our results are in good agreement with available experimental or other simulation data. The effects of interlayer cations (Na+, K+, Ca2+), the cation exchange capacity, and the alkyl chain length on the basal spacing and the structural properties are estimated. These simulations are expected to presage the microstructure of organo-montmorillonite and lead relevant engineering applications.

Structural diversity of marine cyclic peptides and their molecular mechanisms for anticancer, antibacterial, antifungal, and other clinical applications.

PubMed

Lee, Yeji; Phat, Chanvorleak; Hong, Soon-Cheol

2017-09-01

Many cyclic peptides and analogues derived from marine sources are known to possess biological properties, including anticancer, antitumor, antibacterial, antifungal, antiparasitic, anti-inflammation, anti-proliferative, anti-hypertensive, cytotoxic, and antibiotic properties. These compounds demonstrate different activities and modes of action according to their structure such as cyclic oligopeptide, cyclic lipopeptide, cyclic glycopeptide and cyclic depsipeptide. The recent advances in application of the above-mentioned cyclic peptides were reported in dolastatins, soblidotin, didemnin B, aplidine, salinosporamide A, kahalalide F and bryostatin 1 and they are currently in clinical trials. These cyclic peptides are possible novel drugs discovered and developed from marine origin. Literature data concerning the potential properties of marine cyclic peptides were reviewed here, and the structural diversity and biological activities of marine cyclic peptides are discussed in relation to the molecular mechanisms of these marine cyclic peptides. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Properties of Self-Assembled Monolayers Revealed via Inverse Tensiometry.

PubMed

Chen, Jiahao; Wang, Zhengjia; Oyola-Reynoso, Stephanie; Thuo, Martin M

2017-11-28

Self-assembled monolayers (SAMs) have emerged as a simple platform technology and hence have been broadly studied. With advances in state-of-the-art fabrication and characterization methods, new insights into SAM structure and related properties have been delineated, albeit with some discrepancies and/or incoherencies. Some discrepancies, especially between experimental and theoretical work, are in part due to the misunderstanding of subtle structural features such as phase evolution and SAM quality. Recent work has, however, shown that simple techniques, such as the measurement of static contact angles, can be used to delineate otherwise complex properties of the SAM, especially when complemented by other more advanced techniques. In this article, we highlight the effect of nanoscale substrate asperities and molecular chain length on the SAM structure and associated properties. First, surfaces with tunable roughness are prepared on both Au and Ag, and their corresponding n-alkanethiolate SAMs are characterized through wetting and spectroscopy. From these data, chain-length- and substrate-morphology-dependent limits to the odd-even effect (structure and properties vary with the number of carbons in the molecules and the nature of the substrate), parametrization of gauche defect densities, and structural phase evolution (liquidlike, waxy, crystalline interfaces) are deduced. An evaluation of the correlation between the effect of roughness and the components of surface tension (polar-γ p and dispersive-γ d ) reveals that wetting, at nanoscale rough surfaces, evolves proportionally with the ratio of the two components of surface tension. The evolution of conformational order is captured over a range of molecular lengths and parametrized through a dimensionless number, χ c . By deploying a well-known tensiometry technique (herein the liquid is used to characterize the solid, hence the term inverse tensiometry) to characterize SAMs, we demonstrate that complex molecular-level phenomena in SAMs can be understood through simplicity.

Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins

PubMed Central

Jung, Huihun; Pena-Francesch, Abdon; Saadat, Alham; Sebastian, Aswathy; Kim, Dong Hwan; Hamilton, Reginald F.; Albert, Istvan; Allen, Benjamin D.; Demirel, Melik C.

2016-01-01

Many globular and structural proteins have repetitions in their sequences or structures. However, a clear relationship between these repeats and their contribution to the mechanical properties remains elusive. We propose a new approach for the design and production of synthetic polypeptides that comprise one or more tandem copies of a single unit with distinct amorphous and ordered regions. Our designed sequences are based on a structural protein produced in squid suction cups that has a segmented copolymer structure with amorphous and crystalline domains. We produced segmented polypeptides with varying repeat number, while keeping the lengths and compositions of the amorphous and crystalline regions fixed. We showed that mechanical properties of these synthetic proteins could be tuned by modulating their molecular weights. Specifically, the toughness and extensibility of synthetic polypeptides increase as a function of the number of tandem repeats. This result suggests that the repetitions in native squid proteins could have a genetic advantage for increased toughness and flexibility. PMID:27222581

More Than Filaments and Cores: Statistical Study of Structure Formation and Dynamics in Nearby Molecular Clouds

NASA Astrophysics Data System (ADS)

Chen, How-Huan; Goodman, Alyssa

2018-01-01

In the past decade, multiple attempts at understanding the connection between filaments and star forming cores have been made using observations across the entire epectrum. However, the filaments and the cores are usually treated as predefined--and well-defined--entities, instead of structures that often come at different sizes, shapes, with substantially different dynamics, and inter-connected at different scales. In my dissertation, I present an array of studies using different statistical methods, including the dendrogram and the probability distribution function (PDF), of structures at different size scales within nearby molecular clouds. These structures are identified using observations of different density tracers, and where possible, in the multi-dimensional parameter space of key dynamic properties--the LSR velocity, the velocity dispersion, and the column density. The goal is to give an overview of structure formation in nearby star-forming clouds, as well as of the dynamics in these structures. I find that the overall statistical properties of a larger structure is often the summation/superposition of sub-structures within, and that there could be significant variations due to local physical processes. I also find that the star formation process within molecular clouds could in fact take place in a non-monolithic manner, connecting potentially merging and/or transient structures, at different scales.

Machine learning of molecular electronic properties in chemical compound space

NASA Astrophysics Data System (ADS)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Effect of molecular desorption on the electronic properties of self-assembled polarizable molecular monolayers.

PubMed

Wang, Gunuk; Jeong, Hyunhak; Ku, Jamin; Na, Seok-In; Kang, Hungu; Ito, Eisuke; Jang, Yun Hee; Noh, Jaegeun; Lee, Takhee

2014-04-01

We investigated the interfacial electronic properties of self-assembled monolayers (SAM)-modified Au metal surface at elevated temperatures. We observed that the work functions of the Au metal surfaces modified with SAMs changed differently under elevated-temperature conditions based on the type of SAMs categorized by three different features based on chemical anchoring group, molecular backbone structure, and the direction of the dipole moment. The temperature-dependent work function of the SAM-modified Au metal could be explained in terms of the molecular binding energy and the thermal stability of the SAMs, which were investigated with thermal desorption spectroscopic measurements and were explained with molecular modeling. Our study will aid in understanding the electronic properties at the interface between SAMs and metals in organic electronic devices if an annealing treatment is applied. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular Dynamics implementation of BN2D or 'Mercedes Benz' water model

NASA Astrophysics Data System (ADS)

Scukins, Arturs; Bardik, Vitaliy; Pavlov, Evgen; Nerukh, Dmitry

2015-05-01

Two-dimensional 'Mercedes Benz' (MB) or BN2D water model (Naim, 1971) is implemented in Molecular Dynamics. It is known that the MB model can capture abnormal properties of real water (high heat capacity, minima of pressure and isothermal compressibility, negative thermal expansion coefficient) (Silverstein et al., 1998). In this work formulas for calculating the thermodynamic, structural and dynamic properties in microcanonical (NVE) and isothermal-isobaric (NPT) ensembles for the model from Molecular Dynamics simulation are derived and verified against known Monte Carlo results. The convergence of the thermodynamic properties and the system's numerical stability are investigated. The results qualitatively reproduce the peculiarities of real water making the model a visually convenient tool that also requires less computational resources, thus allowing simulations of large (hydrodynamic scale) molecular systems. We provide the open source code written in C/C++ for the BN2D water model implementation using Molecular Dynamics.

Interfacial Molecular Packing Determines Exciton Dynamics in Molecular Heterostructures: The Case of Pentacene-Perfluoropentacene.

PubMed

Rinn, Andre; Breuer, Tobias; Wiegand, Julia; Beck, Michael; Hübner, Jens; Döring, Robin C; Oestreich, Michael; Heimbrodt, Wolfram; Witte, Gregor; Chatterjee, Sangam

2017-12-06

The great majority of electronic and optoelectronic devices depend on interfaces between p-type and n-type semiconductors. Finding matching donor-acceptor systems in molecular semiconductors remains a challenging endeavor because structurally compatible molecules may not necessarily be suitable with respect to their optical and electronic properties, and the large exciton binding energy in these materials may favor bound electron-hole pairs rather than free carriers or charge transfer at an interface. Regardless, interfacial charge-transfer exciton states are commonly considered as an intermediate step to achieve exciton dissociation. The formation efficiency and decay dynamics of such states will strongly depend on the molecular makeup of the interface, especially the relative alignment of donor and acceptor molecules. Structurally well-defined pentacene-perfluoropentacene heterostructures of different molecular orientations are virtually ideal model systems to study the interrelation between molecular packing motifs at the interface and their electronic properties. Comparing the emission dynamics of the heterosystems and the corresponding unitary films enables accurate assignment of every observable emission signal in the heterosystems. These heterosystems feature two characteristic interface-specific luminescence channels at around 1.4 and 1.5 eV that are not observed in the unitary samples. Their emission strength strongly depends on the molecular alignment of the respective donor and acceptor molecules, emphasizing the importance of structural control for device construction.

Exploring the no-man's land between molecular nanomagnets and magnetic nanoparticles.

PubMed

Gatteschi, Dante; Fittipaldi, Maria; Sangregorio, Claudio; Sorace, Lorenzo

2012-05-14

The comparison of the structural and magnetic properties of molecular nanomagnets (MNM) and magnetic nanoparticles (MNP) can be instructive to get a deeper understanding of the magnetic behavior on the intermediate scale between molecular and bulk objects. In this respect iron oxo based clusters are particularly interesting, since they provide an increasing number of molecular systems with sizes close to that of iron oxide MNP. In this Minireview we report a survey of literature data aimed at improving our understanding of the emergence of MNP properties from MNM ones. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Creating and Using a Consumer Chemical Molecular Graphics Database: The "Molecule of the Day" - A Great Way To Begin Your Lecture

NASA Astrophysics Data System (ADS)

Scharberg, Maureen A.; Cox, Oran E.; Barelli, Carl A.

1997-07-01

"The Molecule of the Day" consumer chemical database has been created to allow introductory chemistry students to explore molecular structures of chemicals in household products, and to provide opportunities in molecular modeling for undergraduate chemistry students. Before class begins, an overhead transparency is displayed which shows a three-dimensional molecular structure of a household chemical, and lists relevant features and uses of this chemical. Within answers to questionnaires, students have commented that this molecular graphics database has helped them to visually connect the microscopic structure of a molecule with its physical and chemical properties, as well as its uses in consumer products. It is anticipated that this database will be incorporated into a navigational software package such as Netscape.

Supramolecular Engineering of Hierarchically Self-Assembled, Bioinspired, Cholesteric Nanocomposites Formed by Cellulose Nanocrystals and Polymers.

PubMed

Zhu, Baolei; Merindol, Remi; Benitez, Alejandro J; Wang, Baochun; Walther, Andreas

2016-05-04

Natural composites are hierarchically structured by combination of ordered colloidal and molecular length scales. They inspire future, biomimetic, and lightweight nanocomposites, in which extraordinary mechanical properties are in reach by understanding and mastering hierarchical structure formation as tools to engineer multiscale deformation mechanisms. Here we describe a hierarchically self-assembled, cholesteric nanocomposite with well-defined colloid-based helical structure and supramolecular hydrogen bonds engineered on the molecular level in the polymer matrix. We use reversible addition-fragmentation transfer polymerization to synthesize well-defined hydrophilic, nonionic polymers with a varying functionalization density of 4-fold hydrogen-bonding ureidopyrimidinone (UPy) motifs. We show that these copolymers can be coassembled with cellulose nanocrystals (CNC), a sustainable, stiff, rod-like reinforcement, to give ordered cholesteric phases with characteristic photonic stop bands. The dimensions of the helical pitch are controlled by the ratio of polymer/CNC, confirming a smooth integration into the colloidal structure. With respect to the effect of the supramolecular motifs, we demonstrate that those regulate the swelling when exposing the biomimetic hybrids to water, and they allow engineering the photonic response. Moreover, the amount of hydrogen bonds and the polymer fraction are decisive in defining the mechanical properties. An Ashby plot comparing previous ordered CNC-based nanocomposites with our new hierarchical ones reveals that molecular engineering allows us to span an unprecedented mechanical property range from highest inelastic deformation (strain up to ∼13%) to highest stiffness (E ∼ 15 GPa) and combinations of both. We envisage that further rational design of the molecular interactions will provide efficient tools for enhancing the multifunctional property profiles of such bioinspired nanocomposites.

Inorganic and Organometallic Molecular Wires for Single-Molecule Devices.

PubMed

Tanaka, Yuya; Kiguchi, Manabu; Akita, Munetaka

2017-04-06

Recent developments of single-molecule conductance measurements allow us to understand fundamental conducting properties of molecular wires. While a wide variety of organic molecular wires have been studied so far, inorganic and organometallic molecular wires have received much less attention. However, molecular wires with transition-metal atoms show interesting features and functions distinct from those of organic wires. These properties originate mainly from metal-ligand dπ-pπ interactions and metal-metal d-d interactions. Thanks to the rich combination of metal atoms and supporting ligands, frontier orbital energies of the molecular wires can be finely tuned to lead to highly conducting molecular wires. Moreover, the unique electronic structures of metal complexes are susceptible to subtle environmental changes, leading to potential functional molecular devices. This article reviews recent advances in the single-molecule conductance study of inorganic and organometallic molecular wires. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structures and properties of naturally occurring polyether antibiotics.

PubMed

Rutkowski, Jacek; Brzezinski, Bogumil

2013-01-01

Polyether ionophores represent a large group of natural, biologically active substances produced by Streptomyces spp. They are lipid soluble and able to transport metal cations across cell membranes. Several of polyether ionophores are widely used as growth promoters in veterinary. Polyether antibiotics show a broad spectrum of bioactivity ranging from antibacterial, antifungal, antiparasitic, antiviral, and tumour cell cytotoxicity. Recently, it has been shown that some of these compounds are able to selectively kill cancer stem cells and multidrug-resistant cancer cells. Thus, they are recognized as new potential anticancer drugs. The biological activity of polyether ionophores is strictly connected with their molecular structure; therefore, the purpose of this paper is to present an overview of their formula, molecular structure, and properties.

Structures and Properties of Naturally Occurring Polyether Antibiotics

PubMed Central

Rutkowski, Jacek; Brzezinski, Bogumil

2013-01-01

Polyether ionophores represent a large group of natural, biologically active substances produced by Streptomyces spp. They are lipid soluble and able to transport metal cations across cell membranes. Several of polyether ionophores are widely used as growth promoters in veterinary. Polyether antibiotics show a broad spectrum of bioactivity ranging from antibacterial, antifungal, antiparasitic, antiviral, and tumour cell cytotoxicity. Recently, it has been shown that some of these compounds are able to selectively kill cancer stem cells and multidrug-resistant cancer cells. Thus, they are recognized as new potential anticancer drugs. The biological activity of polyether ionophores is strictly connected with their molecular structure; therefore, the purpose of this paper is to present an overview of their formula, molecular structure, and properties. PMID:23586016

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

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Mechanical design of DNA nanostructures

NASA Astrophysics Data System (ADS)

Castro, Carlos E.; Su, Hai-Jun; Marras, Alexander E.; Zhou, Lifeng; Johnson, Joshua

2015-03-01

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07153k

QSPR models for various physical properties of carbohydrates based on molecular mechanics and quantum chemical calculations.

PubMed

Dyekjaer, Jane Dannow; Jónsdóttir, Svava Osk

2004-01-22

Quantitative Structure-Property Relationships (QSPR) have been developed for a series of monosaccharides, including the physical properties of partial molar heat capacity, heat of solution, melting point, heat of fusion, glass-transition temperature, and solid state density. The models were based on molecular descriptors obtained from molecular mechanics and quantum chemical calculations, combined with other types of descriptors. Saccharides exhibit a large degree of conformational flexibility, therefore a methodology for selecting the energetically most favorable conformers has been developed, and was used for the development of the QSPR models. In most cases good correlations were obtained for monosaccharides. For five of the properties predictions were made for disaccharides, and the predicted values for the partial molar heat capacities were in excellent agreement with experimental values.

Molecular Dynamics Study of Surfactant Self-Assembly on Single-Walled Carbon Nanotubes (SWCNTs)

NASA Astrophysics Data System (ADS)

Phelan, Frederick, Jr.

2015-03-01

Single-walled carbon nanotubes (SWNCTs) are materials with structural, electronic and optical properties that make them attractive for a myriad of advanced technology applications. Increased adaptation of these materials requires advancement in separation techniques which enables them to be sorted with increased reliability into monodisperse fractions with respect to length and chirality. Most separation techniques currently in use rely on dispersion of tubes in aqueous solution using surfactants. This results in a colloidal mixture in which tubes are packed and individually dispersed in a surfactant shell. Understanding the structure and properties of the SWCNT-surfactant complex at the molecular level, and how this is affected by chirality, will help to improve separations processes. In this work, we study the structure and properties of SWCNT-surfactant colloidal complexes using all-atom molecular dynamics. Self-assembled structures are computed for a number of combinations SWCNT/surfactant, and also, co-surfactant mixtures for the bile salt surfactant sodium deoxycholate (DOC) and the anionic surfactant sodium dodecyl sulfate (SDS). From the radial distribution function we estimate the size of the SWCNT hydration layer, and use that information to compute the buoyant densities of unfilled tubes for a number of concentrations. Estimates of the change in hydrodynamic radius with increased surfactant packing and the binding energies of the individual surfactants are also obtained.

THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

Purification, structural characterization and anticoagulant properties of fucosylated chondroitin sulfate isolated from Holothuria mexicana.

PubMed

Mou, Jiaojiao; Wang, Cong; Li, Wenjing; Yang, Jie

2017-05-01

A novel fucosylated chondroitin sulfate (HmG) was isolated from sea cucumber Holothuria mexicana, the structure of which was characterized by monosaccharide composition, disaccharide composition, IR, 1 H and 13 C NMR spectrum, additionally with two dimensional NMR spectrum of degraded HmG (DHmG). The backbone of HmG was identified as chondroitin 6-O sulfate, while the major O-4 sulfated fucose branches linked to O-3 position of glucuronic acid in almost every disaccharide unit. The anticoagulant activities of HmG and DHmG were assessed and compared with heparin and low molecular weight heparin. The results indicated that HmG and DHmG both could significantly prolong the activated partial thrombo-plastin time, and the properties were well related to its molecular weight. DHmG showed similar anticoagulant properties to low molecular weight heparin with less bleeding risks, making it a safer anticoagulant drug. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring parameter space effects on structure-property relationships of surfactants at liquid-liquid interfaces.

PubMed

Emborsky, Christopher P; Cox, Kenneth R; Chapman, Walter G

2011-08-28

The ubiquitous use of surfactants in commercial and industrial applications has led to many experimental, theoretical, and simulation based studies. These efforts seek to provide a molecular level understanding of the effects on structuring behavior and the corresponding impacts on observable properties (e.g., interfacial tension). With such physical detail, targeted system design can be improved over typical techniques of observational trends and phenomenological correlations by taking advantage of predictive system response. This research provides a systematic study of part of the broad parameter space effects on equilibrium microstructure and interfacial properties of amphiphiles at a liquid-liquid interface using the interfacial statistical associating fluid theory density functional theory as a molecular model for the system from the bulk to the interface. Insights into the molecular level physics and thermodynamics governing the system behavior are discussed as they relate to both predictions qualitatively consistent with experimental observations and extensions beyond currently available studies. © 2011 American Institute of Physics

Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

NASA Astrophysics Data System (ADS)

Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

2017-02-01

Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

Adsorption of molecular additive onto lead halide perovskite surfaces: A computational study on Lewis base thiophene additive passivation

NASA Astrophysics Data System (ADS)

Zhang, Lei; Yu, Fengxi; Chen, Lihong; Li, Jingfa

2018-06-01

Organic additives, such as the Lewis base thiophene, have been successfully applied to passivate halide perovskite surfaces, improving the stability and properties of perovskite devices based on CH3NH3PbI3. Yet, the detailed nanostructure of the perovskite surface passivated by additives and the mechanisms of such passivation are not well understood. This study presents a nanoscopic view on the interfacial structure of an additive/perovskite interface, consisting of a Lewis base thiophene molecular additive and a lead halide perovskite surface substrate, providing insights on the mechanisms that molecular additives can passivate the halide perovskite surfaces and enhance the perovskite-based device performance. Molecular dynamics study on the interactions between water molecules and the perovskite surfaces passivated by the investigated additive reveal the effectiveness of employing the molecular additives to improve the stability of the halide perovskite materials. The additive/perovskite surface system is further probed via molecular engineering the perovskite surfaces. This study reveals the nanoscopic structure-property relationships of the halide perovskite surface passivated by molecular additives, which helps the fundamental understanding of the surface/interface engineering strategies for the development of halide perovskite based devices.

Effects of countercations on the structures and redox and spectroscopic properties of diruthenium catecholate complexes with ligand-unsupported Ru-Ru bonds.

PubMed

Chang, Ho-Chol; Mochizuki, Katsunori; Kitagawa, Susumu

2005-05-30

The molecular structures and physicochemical properties of diruthenium complexes with ligand-unsupported Ru-Ru bonds, generally formulated as [A2{Ru2(DTBCat)4}] (DTB = 3,5- or 3,6-di-tert-butyl; Cat(2-) = catecholate), were studied in detail by changing the countercations. First, the binding structures of the cations in a family of [{A(DME)n}2{Ru2(3,5-DTBCat)4}] (n = 2 for A+ = Li+ and Na+ and n = 1 for A+ = K+ and Rb+) were systematically examined to reveal the effects of the cations on the molecular structures and electrochemical properties. Second, the complex (n-Bu4N)2[Ru2(3,6-DTBCat)4] with a cation-free structure was synthesized using tetra-n-butylammonium cations. The complex clearly demonstrates first that the ligand-unsupported Ru-Ru bonds are essentially stabilized by the dianionic nature of the catecholate derivatives without any other bridging or supporting species. In contrast, the redox potentials and absorption spectra of the complexes can sensitively respond to the countercations depending upon the polarity of the solvents.

Molecular dynamics study of silicon carbide properties under external dynamic loading

NASA Astrophysics Data System (ADS)

Utkin, A. V.; Fomin, V. M.

2017-10-01

In this study, molecular dynamic simulations of high-velocity impact of a spherical 3C-SiC cluster, with a wide range of velocities (from 100 to 2600 m/s) and with a rigid wall, were performed. The analysis of the final structure shows that no structural phase transformation occurred in the material, despite the high pressure during the collision process.

DemQSAR: predicting human volume of distribution and clearance of drugs

NASA Astrophysics Data System (ADS)

Demir-Kavuk, Ozgur; Bentzien, Jörg; Muegge, Ingo; Knapp, Ernst-Walter

2011-12-01

In silico methods characterizing molecular compounds with respect to pharmacologically relevant properties can accelerate the identification of new drugs and reduce their development costs. Quantitative structure-activity/-property relationship (QSAR/QSPR) correlate structure and physico-chemical properties of molecular compounds with a specific functional activity/property under study. Typically a large number of molecular features are generated for the compounds. In many cases the number of generated features exceeds the number of molecular compounds with known property values that are available for learning. Machine learning methods tend to overfit the training data in such situations, i.e. the method adjusts to very specific features of the training data, which are not characteristic for the considered property. This problem can be alleviated by diminishing the influence of unimportant, redundant or even misleading features. A better strategy is to eliminate such features completely. Ideally, a molecular property can be described by a small number of features that are chemically interpretable. The purpose of the present contribution is to provide a predictive modeling approach, which combines feature generation, feature selection, model building and control of overtraining into a single application called DemQSAR. DemQSAR is used to predict human volume of distribution (VDss) and human clearance (CL). To control overtraining, quadratic and linear regularization terms were employed. A recursive feature selection approach is used to reduce the number of descriptors. The prediction performance is as good as the best predictions reported in the recent literature. The example presented here demonstrates that DemQSAR can generate a model that uses very few features while maintaining high predictive power. A standalone DemQSAR Java application for model building of any user defined property as well as a web interface for the prediction of human VDss and CL is available on the webpage of DemPRED: http://agknapp.chemie.fu-berlin.de/dempred/.

DemQSAR: predicting human volume of distribution and clearance of drugs.

PubMed

Demir-Kavuk, Ozgur; Bentzien, Jörg; Muegge, Ingo; Knapp, Ernst-Walter

2011-12-01

In silico methods characterizing molecular compounds with respect to pharmacologically relevant properties can accelerate the identification of new drugs and reduce their development costs. Quantitative structure-activity/-property relationship (QSAR/QSPR) correlate structure and physico-chemical properties of molecular compounds with a specific functional activity/property under study. Typically a large number of molecular features are generated for the compounds. In many cases the number of generated features exceeds the number of molecular compounds with known property values that are available for learning. Machine learning methods tend to overfit the training data in such situations, i.e. the method adjusts to very specific features of the training data, which are not characteristic for the considered property. This problem can be alleviated by diminishing the influence of unimportant, redundant or even misleading features. A better strategy is to eliminate such features completely. Ideally, a molecular property can be described by a small number of features that are chemically interpretable. The purpose of the present contribution is to provide a predictive modeling approach, which combines feature generation, feature selection, model building and control of overtraining into a single application called DemQSAR. DemQSAR is used to predict human volume of distribution (VD(ss)) and human clearance (CL). To control overtraining, quadratic and linear regularization terms were employed. A recursive feature selection approach is used to reduce the number of descriptors. The prediction performance is as good as the best predictions reported in the recent literature. The example presented here demonstrates that DemQSAR can generate a model that uses very few features while maintaining high predictive power. A standalone DemQSAR Java application for model building of any user defined property as well as a web interface for the prediction of human VD(ss) and CL is available on the webpage of DemPRED: http://agknapp.chemie.fu-berlin.de/dempred/ .

Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Xie, Quan; Tian, Zean; Chen, Qian; Liang, Yongchao; Ren, Lei; Hu, Xuechen

2018-01-01

The growth of GaN crystals at different pressures was studied by molecular dynamics simulation employing the Stillinger-Weber potential, and their structural properties and defects were characterized using the radial distribution function, the Voronoi polyhedron index method, and a suitable visualization technology. Crystal structures formed at 0, 1, 5, 10, and 20 GPa featured an overwhelming number of <4 0 0 0> Voronoi polyhedra, whereas amorphous structures comprising numerous disordered polyhedra were produced at 50 GPa. During quenching, coherent twin boundaries were easily formed between zinc-blende and wurtzite crystal structures in GaN. Notably, point defects usually appeared at low pressure, whereas dislocations were observed at high pressure, since the simultaneous growth of two crystal grains with different crystal orientations and their boundary expansion was hindered in the latter case, resulting in the formation of a dislocation between these grains.

Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings.

PubMed

Jensen, Malene Ringkjøbing; Markwick, Phineus R L; Meier, Sebastian; Griesinger, Christian; Zweckstetter, Markus; Grzesiek, Stephan; Bernadó, Pau; Blackledge, Martin

2009-09-09

Intrinsically disordered proteins (IDPs) inhabit a conformational landscape that is too complex to be described by classical structural biology, posing an entirely new set of questions concerning the molecular understanding of functional biology. The characterization of the conformational properties of IDPs, and the elucidation of the role they play in molecular function, is therefore one of the major challenges remaining for modern structural biology. NMR is the technique of choice for studying this class of proteins, providing information about structure, flexibility, and interactions at atomic resolution even in completely disordered states. In particular, residual dipolar couplings (RDCs) have been shown to be uniquely sensitive and powerful tools for characterizing local and long-range structural behavior in disordered proteins. In this review we describe recent applications of RDCs to quantitatively describe the level of local structure and transient long-range order in IDPs involved in viral replication, neurodegenerative disease, and cancer.

Theoretical investigations of molecular wires: Electronic spectra and electron transport

NASA Astrophysics Data System (ADS)

Palma, Julio Leopoldo

The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with respect to the azo group. The results showed that the molecular structure is crucial in optimizing the electron transport properties of chemical structures, and that the transport properties in electronic devices at the molecular level can be manipulated, enhanced or suppressed by a careful consideration of the effects of chemical modification.

Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

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

Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed

2016-05-06

The molecular structure of fullerene (C{sub 60}) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electronmore » affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.« less

Nanotechnology Presentation Agenda

NASA Technical Reports Server (NTRS)

2005-01-01

Working at the atomic, molecular and supra-molecular levels, in the length scale of approximately 1 - 100 nm range, in order to understand, create and use materials, devices and systems with fundamentally new properties and functions because of their small structure. NNI definition encourages new contributions that were not possible.before. Novel phenomena, properties and functions at nanoscale,which are non scalable outside of the nm domain. The ability to measure / control / manipulate matter at the nanoscale in order to change those properties and functions. Integration along length scales, and fields of application.

Hybrid organic-inorganic rotaxanes and molecular shuttles.

PubMed

Lee, Chin-Fa; Leigh, David A; Pritchard, Robin G; Schultz, David; Teat, Simon J; Timco, Grigore A; Winpenny, Richard E P

2009-03-19

The tetravalency of carbon and its ability to form covalent bonds with itself and other elements enables large organic molecules with complex structures, functions and dynamics to be constructed. The varied electronic configurations and bonding patterns of inorganic elements, on the other hand, can impart diverse electronic, magnetic, catalytic and other useful properties to molecular-level structures. Some hybrid organic-inorganic materials that combine features of both chemistries have been developed, most notably metal-organic frameworks, dense and extended organic-inorganic frameworks and coordination polymers. Metal ions have also been incorporated into molecules that contain interlocked subunits, such as rotaxanes and catenanes, and structures in which many inorganic clusters encircle polymer chains have been described. Here we report the synthesis of a series of discrete rotaxane molecules in which inorganic and organic structural units are linked together mechanically at the molecular level. Structural units (dialkyammonium groups) in dumb-bell-shaped organic molecules template the assembly of essentially inorganic 'rings' about 'axles' to form rotaxanes consisting of various numbers of rings and axles. One of the rotaxanes behaves as a 'molecular shuttle': the ring moves between two binding sites on the axle in a large-amplitude motion typical of some synthetic molecular machine systems. The architecture of the rotaxanes ensures that the electronic, magnetic and paramagnetic characteristics of the inorganic rings-properties that could make them suitable as qubits for quantum computers-can influence, and potentially be influenced by, the organic portion of the molecule.

Vibrational, structural and electronic properties investigation by DFT calculations and molecular docking studies with DNA topoisomerase II of strychnobrasiline type alkaloids: A theoretical approach for potentially bioactive molecules

NASA Astrophysics Data System (ADS)

Costa, Renyer A.; Oliveira, Kelson M. T.; Costa, Emmanoel Vilaça; Pinheiro, Maria L. B.

2017-10-01

A combined experimental and theoretical DFT study of the structural, vibrational and electronic properties of strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline is presented using the Becke three-parameter Lee-Yang-Parr function (B3LYP) and 6-311G(2d,p) basis set. The theoretical geometry optimization data were compared with the X-ray data for a similar structure in the associated literature, showing close values. The calculated HOMO-LUMO gap values showed that the presence of substituents in the benzene ring influences the quantum properties which are directly related to the reactive properties. Theoretical UV spectra agreed well with the measured experimental data, with bands assigned. In addition, Natural Bond Orbitals (NBOs), Mapped molecular electrostatic potential surface (MEPS) and NLO calculations were also performed at the same theory level. The theoretical vibrational analysis revealed several characteristic vibrations that may be used as a diagnostic tool for other strychnobrasiline type alkaloids, simplifying their identification and structural characterization. Molecular docking calculations with DNA Topoisomerase II-DNA complex showed binding free energies values of -8.0 and -9.5 kcal/mol for strychnobrasiline and 12-hydroxy-10,11-dimethoxystrychnobrasiline respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of -10.0 kcal/mol, suggesting that strychnobrasiline derivative alkaloids might exhibit an antineoplastic activity.

Analysis of the mechanical behavior of single wall carbon nanotubes by a modified molecular structural mechanics model incorporating an advanced chemical force field

NASA Astrophysics Data System (ADS)

Eberhardt, Oliver; Wallmersperger, Thomas

2018-03-01

The outstanding properties of carbon nanotubes (CNTs) keep attracting the attention of researchers from different fields. CNTs are promising candidates for applications e.g. in lightweight construction but also in electronics, medicine and many more. The basis for the realization of the manifold applications is a detailed knowledge of the material properties of the carbon nanotubes. In particular for applications in lightweight constructions or in composites, the knowledge of the mechanical behavior of the CNTs is of vital interest. Hence, a lot of effort is put into the experimental and theoretical determination of the mechanical material properties of CNTs. Due to their small size, special techniques have to be applied. In this research, a modified molecular structural mechanics model for the numerical determination of the mechanical behavior of carbon nanotubes is presented. It uses an advanced approach for the geometrical representation of the CNT structure while the covalent bonds in the CNTs are represented by beam elements. Furthermore, the model is specifically designed to overcome major drawbacks in existing molecular structural mechanics models. This includes energetic consistency with the underlying chemical force field. The model is developed further to enable the application of a more advanced chemical force field representation. The developed model is able to predict, inter alia, the lateral and radial stiffness properties of the CNTs. The results for the lateral stiffness are given and discussed in order to emphasize the progress made with the presented approach.

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

ERIC Educational Resources Information Center

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

ESTIMATION OF PHYSIOCHEMICAL PROPERTIES OF ORGANIC COMPOUNDS BY 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...

First-principles investigation on structural and electronic properties of antimonene nanoribbons and nanotubes

NASA Astrophysics Data System (ADS)

Nagarajan, V.; Chandiramouli, R.

2018-03-01

The electronic properties of antimonene nanotubes and nanoribbons hydrogenated along the zigzag and armchair borders are investigated with the help of density functional theory (DFT) method. The structural stability of antimonene nanostructures is confirmed with the formation energy. The electronic properties of hydrogenated zigzag and armchair antimonene nanostructures are studied in terms of highest occupied molecular orbital (HOMO) & lowest unoccupied molecular orbital (LUMO) gap and density of states (DOS) spectrum. Moreover, due to the influence of buckled orientation, hydrogen passivation and width of antimonene nanostructures, the HOMO-LUMO gap widens in the range of 0.15-0.41 eV. The findings of the present study confirm that the electronic properties of antimonene nanostructures can be tailored with the influence of width, orientation of the edges, passivation with hydrogen and morphology of antimonene nanostructures (nanoribbons, nanotubes), which can be used as chemical sensor and for spintronic devices.

Recent advances in magnetic resonance microscopy to the physical structure characterization of carbonaceous and inorganic materials

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

Gregory, D.M.; Gerald, R.E.; Cody, G.D.

1997-04-01

Magnetic resonance microscopy (MRM) techniques have been employed to study the molecular architectures and properties of structural polymers, fossil fuels, microporous carbons and inorganic catalysts.

Charge delocalization characteristics of regioregular high mobility polymers

DOE PAGES

Coughlin, J. E.; Zhugayevych, A.; Wang, M.; ...

2017-01-01

Controlling the regioregularity among the structural units of narrow bandgap conjugated polymer backbones has led to improvements in optoelectronic properties, for example in the mobilities observed in field effect transistor devices. To investigate how the regioregularity affects quantities relevant to hole transport, regioregular and regiorandom oligomers representative of polymeric structures were studied using density functional theory. Several structural and electronic characteristics of the oligomers were compared, including chain planarity, cation spin density, excess charges on molecular units and internal reorganizational energy. The main difference between the regioregular and regiorandom oligomers is found to be the conjugated backbone planarity, while themore » reorganizational energies calculated are quite similar across the molecular family. Lastly, this work constitutes the first step on understanding the complex interplay of atomistic changes and an oligomer backbone structure toward modeling the charge transport properties.« less

Study of the structural and optical properties of GaP(N) layers synthesized by molecular-beam epitaxy on Si(100) 4° substrates

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

Kryzhanovskaya, N. V., E-mail: NataliaKryzh@gmail.com; Polubavkina, Yu. S.; Nevedomskiy, V. N.

The structural and optical properties of GaP and GaPN layers synthesized by molecular-beam epitaxy on Si(100) substrates misoriented by 4° are studied. The possibility of producing GaP buffer layers that exhibit a high degree of heterointerface planarity and an outcropping dislocation density of no higher than ~2 × 10{sup 8} cm{sup –2} is shown. Emission from the Si/GaP/GaPN structure in the spectral range of 630–640 nm at room temperature is observed. Annealing during growth of the Si/GaP/GaPN structure makes it possible to enhance the room-temperature photoluminescence intensity by a factor of 2.6, with no shift of the maximum of themore » emission line.« less

Atomistic modeling of mechanical properties of polycrystalline graphene.

PubMed

Mortazavi, Bohayra; Cuniberti, Gianaurelio

2014-05-30

We performed molecular dynamics (MD) simulations to investigate the mechanical properties of polycrystalline graphene. By constructing molecular models of ultra-fine-grained graphene structures, we studied the effect of different grain sizes of 1-10 nm on the mechanical response of graphene. We found that the elastic modulus and tensile strength of polycrystalline graphene decrease with decreasing grain size. The calculated mechanical proprieties for pristine and polycrystalline graphene sheets are found to be in agreement with experimental results in the literature. Our MD results suggest that the ultra-fine-grained graphene structures can show ultrahigh tensile strength and elastic modulus values that are very close to those of pristine graphene sheets.

Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

PubMed

Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

2008-11-05

A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

PubMed

Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

2015-02-01

Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications.

Molecular switches and motors on surfaces.

PubMed

Pathem, Bala Krishna; Claridge, Shelley A; Zheng, Yue Bing; Weiss, Paul S

2013-01-01

Molecular switches and motors respond structurally, electronically, optically, and/or mechanically to external stimuli, testing and potentially enabling extreme miniaturization of optoelectronic devices, nanoelectromechanical systems, and medical devices. The assembly of motors and switches on surfaces makes it possible both to measure the properties of individual molecules as they relate to their environment and to couple function between assembled molecules. In this review, we discuss recent progress in assembling molecular switches and motors on surfaces, measuring static and dynamic structures, understanding switching mechanisms, and constructing functional molecular materials and devices. As demonstrative examples, we choose a representative molecule from three commonly studied classes including molecular switches, photochromic molecules, and mechanically interlocked molecules. We conclude by offering perspectives on the future of molecular switches and motors on surfaces.

DNA-Based Single-Molecule Electronics: From Concept to Function.

PubMed

Wang, Kun

2018-01-17

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I-V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

DNA-Based Single-Molecule Electronics: From Concept to Function

PubMed Central

2018-01-01

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed. PMID:29342091

Quantum chemical and statistical study of megazol-derived compounds with trypanocidal activity

NASA Astrophysics Data System (ADS)

Rosselli, F. P.; Albuquerque, C. N.; da Silva, A. B. F.

In this work we performed a structure-activity relationship (SAR) study with the aim to correlate molecular properties of the megazol compound and 10 of its analogs with the biological activity against Trypanosoma cruzi (trypanocidal or antichagasic activity) presented by these molecules. The biological activity indication was obtained from in vitro tests and the molecular properties (variables or descriptors) were obtained from the optimized chemical structures by using the PM3 semiempirical method. It was calculated ˜80 molecular properties selected among steric, constitutional, electronic, and lipophilicity properties. In order to reduce dimensionality and investigate which subset of variables (descriptors) would be more effective in classifying the compounds studied, according to their degree of trypanocidal activity, we employed statistical methodologies (pattern recognition and classification techniques) such as principal component analysis (PCA), hierarchical cluster analysis (HCA), K-nearest neighbor (KNN), and discriminant function analysis (DFA). These methods showed that the descriptors molecular mass (MM), energy of the second lowest unoccupied molecular orbital (LUMO+1), charge on the first nitrogen at substituent 2 (qN'), dihedral angles (D1 and D2), bond length between atom C4 and its substituent (L4), Moriguchi octanol-partition coefficient (MLogP), and length-to-breadth ratio (L/Bw) were the variables responsible for the separation between active and inactive compounds against T. cruzi. Afterwards, the PCA, KNN, and DFA models built in this work were used to perform trypanocidal activity predictions for eight new megazol analog compounds.

Nanogap structures for molecular nanoelectronics

PubMed Central

2012-01-01

This study is focused on the realization of nanodevices for nano and molecular electronics, based on molecular interactions in a metal-molecule-metal (M-M-M) structure. In an M-M-M system, the electronic function is a property of the structure and can be characterized through I/V measurements. The contact between the metals and the molecule was obtained by gold nanogaps (with a dimension of less than 10 nm), produced with the electromigration technique. The nanogap fabrication was controlled by a custom hardware and the related software system. The studies were carried out through experiments and simulations of organic molecules, in particular oligothiophenes. PMID:22321736

Molecular Modeling of a Probe in 2D IR Spectroscopy

NASA Astrophysics Data System (ADS)

Cooper, Anthony; Larini, Luca

Proteins must adopt a precise three dimensional structure in the folding process in order to perform its designated function. Although much has been learned about folding, there are still many details in structural dynamics that are difficult to characterize by existing experimental techniques. In order to overcome these challenges, novel infrared and fluorescent spectroscopic techniques have recently been employed to probe the molecular structure at the atomistic scale. These techniques rely on the spectroscopic properties of the nitrile group attached to a phenylalanine. In this study, we model this probe and we compute its properties in different solvents. This is done by performing Molecular Dynamics simulations with a PheCN solvated in water, urea and TMAO. We measure the decay rate of the vibrational stretching of the CN group in order to characterize the effects of different solvents on the local structure of the molecule. This data can be used to identify non-trivial conformational changes of the protein in the folding process. Preliminary results show agreement with current experimental data on 2D IR spectroscopy.

Physical vapor deposition as a route to glasses with liquid crystalline order

NASA Astrophysics Data System (ADS)

Gomez, Jaritza

Physical vapor deposition (PVD) is an effective route to prepare glasses with a unique combination of properties. Substrate temperatures near the glass transition (Tg) and slow deposition rates can access enhanced mobility at the surface of the glass allowing molecules at the surface additional time to sample different molecular configurations. The temperature of the substrate can be used to control molecular mobility during deposition and properties in the resulting glasses such as higher density, kinetic stability and preferential molecular orientation. PVD was used to prepare glasses of itraconazole, a smectic A liquid crystal. We characterized molecular orientation using infrared and ellipsometry. Molecular orientation can be controlled by choice of Tsubstrate in a range of temperatures near Tg. Glasses deposited at Tsubstrate = Tg show nearly vertical molecular orientation relative to the substrate; at lower Tsubstrate, molecules are nearly parallel to the substrate. The molecular orientation depends on the temperature of the substrate during preparation and not on the molecular orientation of the underlying layer. This allows preparing samples of layers with differing orientations. We find these glasses are homogeneous solids without evidence of domain boundaries and are molecularly flat. We interpret the combination of properties obtained for vapor-deposited glasses of itraconazole to result from a process where molecular orientation is determined by the structure and dynamics at the free surface of the glass during deposition. We report the thermal and structural properties of glasses prepared using PVD of a rod-like molecule, posaconazole, which does not show equilibrium liquid crystal phases. These glasses show substantial molecular orientation that can be controlled by choice of Tsubstrate during deposition. Ellipsometry and IR indicate that glasses prepared at Tg - 3 K are highly ordered. At these Tsubstrate, molecules show preferential vertical orientation and orientation is similar to that measured in aligned nematic liquid crystal. Our results are consistent with a recently proposed mechanism where molecular orientation in equilibrium liquids can be trapped in PVD glasses and suggest that the orientation at the free surface of posaconazole is nematic-like. In addition, we show posaconazole glasses show high kinetic stability controlled by Tsubstrate.

Heteroatom-bridged benzothiazolyls for organic solar cells: a theoretical study.

PubMed

Chen, Runfeng; Wang, Yang; Chen, Ting; Li, Huanhuan; Zheng, Chunhua; Yuan, Kai; Wang, Zhixiang; Tao, Ye; Zheng, Chao; Huang, Wei

2015-01-15

On the basis of a typical organic photovoltaic (OPV) building block of 4,7-di(thiophen-2-yl)benzo[c][1,2,5]thiadiazole (DTBT), a series of novel DTBT derivatives were designed following a heteroatom-bridging strategy to take advantage of the diversified interactions between heteroatoms and π-conjugated systems. These heteroatom-bridged DTBTs, whose outer electron-rich thiophene moieties are covalently fastened to the central electron-deficient benzothiadiazole with additional heteroatom bridges, exhibit promising features for OPV applications with rigid molecular structures, properly lain frontier molecular orbitals (FMOs), broad and intense absorption spectra, and adequate charge transport properties, as revealed by systematic theoretical calculations on molecular geometries, FMOs, absorption spectra, and relaxation and reorganization energies. The structure-property relationship investigations show that the mono-/di-heteroatom bridging is effective not only in tuning the rigidity of the molecular geometries but also in adjusting the optoelectronic properties of the resulting materials. Among the studied heteroatoms, the C and Si were found to be the most efficient in designing novel molecules for OPV applications. These theoretical insights may provide a solid basis for experimental synthesis and device investigations of the proposed heteroatom-bridged DTBTs as potential high-performance building blocks for bulk heterojunction OPV molecules.

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.

Interferometric 2D Sum Frequency Generation Spectroscopy Reveals Structural Heterogeneity of Catalytic Monolayers on Transparent Materials.

PubMed

Vanselous, Heather; Stingel, Ashley M; Petersen, Poul B

2017-02-16

Molecular monolayers exhibit structural and dynamical properties that are different from their bulk counterparts due to their interaction with the substrate. Extracting these distinct properties is crucial for a better understanding of processes such as heterogeneous catalysis and interfacial charge transfer. Ultrafast nonlinear spectroscopic techniques such as 2D infrared (2D IR) spectroscopy are powerful tools for understanding molecular dynamics in complex bulk systems. Here, we build on technical advancements in 2D IR and heterodyne-detected sum frequency generation (SFG) spectroscopy to study a CO 2 reduction catalyst on nanostructured TiO 2 with interferometric 2D SFG spectroscopy. Our method combines phase-stable heterodyne detection employing an external local oscillator with a broad-band pump pulse pair to provide the first high spectral and temporal resolution 2D SFG spectra of a transparent material. We determine the overall molecular orientation of the catalyst and find that there is a static structural heterogeneity reflective of different local environments at the surface.

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

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

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Mesoscale Graphene-like Honeycomb Mono- and Multilayers Constructed via Self-Assembly of Coclusters.

PubMed

Hou, Xue-Sen; Zhu, Guo-Long; Ren, Li-Jun; Huang, Zi-Han; Zhang, Rui-Bin; Ungar, Goran; Yan, Li-Tang; Wang, Wei

2018-02-07

Honeycomb structure endows graphene with extraordinary properties. But could a honeycomb monolayer superlattice also be generated via self-assembly of colloids or nanoparticles? Here we report the construction of mono- and multilayer molecular films with honeycomb structure that can be regarded as self-assembled artificial graphene (SAAG). We construct fan-shaped molecular building blocks by covalently connecting two kinds of clusters, one polyoxometalate and four polyhedral oligomeric silsesquioxanes. The precise shape control enables these complex molecules to self-assemble into a monolayer 2D honeycomb superlattice that mirrors that of graphene but on the mesoscale. The self-assembly of the SAAG was also reproduced via coarse-grained molecular simulations of a fan-shaped building block. It revealed a hierarchical process and the key role of intermediate states in determining the honeycomb structure. Experimental images also show a diversity of bi- and trilayer stacking modes. The successful creation of SAAG and its stacks opens up prospects for the preparation of novel self-assembled nanomaterials with unique properties.

Mechanical properties and the electronic structure of transition of metal alloys

NASA Technical Reports Server (NTRS)

Arsenault, R. J.; Drew, H. D.

1977-01-01

This interdiscipline research program was undertaken in an effort to investigate the relationship between the mechanical strength of Mo based alloys with their electronic structure. Electronic properties of these alloys were examined through optical studies, and the classical solid solution strengthening mechanisms were considered, based on size and molecular differences to determine if these mechanisms could explain the hardness data.

Mechanical features of various silkworm crystalline considering hydration effect via molecular dynamics simulations.

PubMed

Kim, Yoonjung; Lee, Myeongsang; Choi, Hyunsung; Baek, Inchul; Kim, Jae In; Na, Sungsoo

2018-04-01

Silk materials are receiving significant attention as base materials for various functional nanomaterials and nanodevices, due to its exceptionally high mechanical properties, biocompatibility, and degradable characteristics. Although crystalline silk regions are composed of various repetitive motifs with differing amino acid sequences, how the effect of humidity works differently on each of the motifs and their structural characteristics remains unclear. We report molecular dynamics (MD) simulations on various silkworm fibroins composed of major motifs (i.e. (GAGAGS) n , (GAGAGA) n , and (GAGAGY) n ) at varying degrees of hydration, and reveal how each major motifs of silk fibroins change at each degrees of hydration using MD simulations and their structural properties in mechanical perspective via steered molecular dynamics simulations. Our results explain what effects humidity can have on nanoscale materials and devices consisting of crystalline silk materials.

Synthesis of Structurally Diverse Emissive Molecular Rotors with Four-Component Ugi Stators.

PubMed

García-González, Ma Carmen; Aguilar-Granda, Andrés; Zamudio-Medina, Angel; Miranda, Luis D; Rodríguez-Molina, Braulio

2018-03-02

The use of the multicomponent Ugi reaction to rapidly prepare a library of dumbbell-like molecular rotors is highlighted here. The synthetic strategy consisted of the atom-economic access to 15 bulky and structurally diverse iodinated stators, which were cross-coupled to the 1,4-diethynylphenylene rotator. From those experiments, up to six rotors 1a-c and 1l-n were obtained, with yields ranging from 35 to 69% per coupled C-C bond. In addition to the framework diversity, five of these compounds showed aggregate-enhanced emission properties thanks to their conjugated 1,4-bis(phenylethynyl)benzene cores, a property that rises by increasing the water fraction (f w ) in their THF solutions. The results highlight the significance of the diversity-oriented synthesis of rapid access to new molecular fluorescent rotors.

Synthetic polymers and biomembranes. How do they interact? Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer.

PubMed

Pal, Sandeep; Milano, Giuseppe; Roccatano, Danilo

2006-12-28

The understanding of interactions of poly(ethylene glycol) (PEG) or poly(ethylene oxide) (PEO) with biological interfaces has important technological application in industry and in medicine. In this paper, structural and dynamical properties of PEO at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface have been investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The structural properties of a PEO chain in bulk water, at the water/vacuum interface, and in the presence of the membrane were compared with available experimental data. The presence of a barrier for the PEO penetration into the DMPC bilayer has been found. A qualitative estimation of the barrier provided a value equal to approximately 19 kJ/mol, that is, 7 times the value of kT at 310 K.

Potential for protein surface shape analysis using spherical harmonics and 3D Zernike descriptors.

PubMed

Venkatraman, Vishwesh; Sael, Lee; Kihara, Daisuke

2009-01-01

With structure databases expanding at a rapid rate, the task at hand is to provide reliable clues to their molecular function and to be able to do so on a large scale. This, however, requires suitable encodings of the molecular structure which are amenable to fast screening. To this end, moment-based representations provide a compact and nonredundant description of molecular shape and other associated properties. In this article, we present an overview of some commonly used representations with specific focus on two schemes namely spherical harmonics and their extension, the 3D Zernike descriptors. Key features and differences of the two are reviewed and selected applications are highlighted. We further discuss recent advances covering aspects of shape and property-based comparison at both global and local levels and demonstrate their applicability through some of our studies.

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

DNA nanotechnology and fluorescence applications.

PubMed

Schlichthaerle, Thomas; Strauss, Maximilian T; Schueder, Florian; Woehrstein, Johannes B; Jungmann, Ralf

2016-06-01

Structural DNA nanotechnology allow researchers to use the unique molecular recognition properties of DNA strands to construct nanoscale objects with almost arbitrary complexity in two and three dimensions. Abstracted as molecular breadboards, DNA nanostructures enable nanometer-precise placement of guest molecules such as proteins, fluorophores, or nanoparticles. These assemblies can be used to study biological phenomena with unprecedented control over number, spacing, and molecular identity. Here, we give a general introduction to structural DNA nanotechnology and more specifically discuss applications of DNA nanostructures in the field of fluorescence and plasmonics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Hall-Effect Measurements Probing the Degree of Charge-Carrier Delocalization in Solution-Processed Crystalline Molecular Semiconductors

NASA Astrophysics Data System (ADS)

Chang, Jui-Fen; Sakanoue, Tomo; Olivier, Yoann; Uemura, Takafumi; Dufourg-Madec, Marie-Beatrice; Yeates, Stephen G.; Cornil, Jérôme; Takeya, Jun; Troisi, Alessandro; Sirringhaus, Henning

2011-08-01

Intramolecular structure and intermolecular packing in crystalline molecular semiconductors should have profound effects on the charge-carrier wave function, but simple drift mobility measurements are not very sensitive to this. Here we show that differences in the Hall resistance of two soluble pentacene derivatives can be explained with different degrees of carrier delocalization being limited by thermal lattice fluctuations. A combination of Hall measurements, optical spectroscopy, and theoretical simulations provides a powerful probe of structure-property relationships at a molecular level.

The composite hydrogels of polyvinyl alcohol-gellan gum-Ca(2+) with improved network structure and mechanical property.

PubMed

Wang, Fei; Wen, Ying; Bai, Tongchun

2016-12-01

The composite hydrogels of polyvinyl alcohol (PVA) and gellan gum (GG) are of interesting in the biomaterials application. To improve the structure and mechanical property, in this work, Ca(2+) ion was introduced to crosslink the polymer chain, and the PVA-GG-Ca(2+) hydrogel was formed. By analyzing its structure, mechanical properties, swelling and dehydration kinetics, the effect of molecular interaction on hydrogel structure and properties have been observed. Our result indicates that, as GG is added to hydrogel network, the role of Ca(2+) ion is stand out, it reorganizes the network structure, enhances the mechanical properties, and strengthens the electrolytic and hydrogen bonding interactions in PVA-GG-Ca(2+) hydrogels. These observations will benefit the development of hydrogels in biomaterials application. Copyright © 2016. Published by Elsevier B.V.

Quantitative structure-property relationship modeling of Grätzel solar cell dyes.

PubMed

Venkatraman, Vishwesh; Åstrand, Per-Olof; Alsberg, Bjørn Kåre

2014-01-30

With fossil fuel reserves on the decline, there is increasing focus on the design and development of low-cost organic photovoltaic devices, in particular, dye-sensitized solar cells (DSSCs). The power conversion efficiency (PCE) of a DSSC is heavily influenced by the chemical structure of the dye. However, as far as we know, no predictive quantitative structure-property relationship models for DSSCs with PCE as one of the response variables have been reported. Thus, we report for the first time the successful application of comparative molecular field analysis (CoMFA) and vibrational frequency-based eigenvalue (EVA) descriptors to model molecular structure-photovoltaic performance relationships for a set of 40 coumarin derivatives. The results show that the models obtained provide statistically robust predictions of important photovoltaic parameters such as PCE, the open-circuit voltage (V(OC)), short-circuit current (J(SC)) and the peak absorption wavelength λ(max). Some of our findings based on the analysis of the models are in accordance with those reported in the literature. These structure-property relationships can be applied to the rational structural design and evaluation of new photovoltaic materials. Copyright © 2013 Wiley Periodicals, Inc.

ALMA Observations of a Quiescent Molecular Cloud in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Wong, Tony; Hughes, Annie; Tokuda, Kazuki; Indebetouw, Rémy; Bernard, Jean-Philippe; Onishi, Toshikazu; Wojciechowski, Evan; Bandurski, Jeffrey B.; Kawamura, Akiko; Roman-Duval, Julia; Cao, Yixian; Chen, C.-H. Rosie; Chu, You-hua; Cui, Chaoyue; Fukui, Yasuo; Montier, Ludovic; Muller, Erik; Ott, Juergen; Paradis, Deborah; Pineda, Jorge L.; Rosolowsky, Erik; Sewiło, Marta

2017-12-01

We present high-resolution (subparsec) observations of a giant molecular cloud in the nearest star-forming galaxy, the Large Magellanic Cloud. ALMA Band 6 observations trace the bulk of the molecular gas in 12CO(2-1) and the high column density regions in 13CO(2-1). Our target is a quiescent cloud (PGCC G282.98-32.40, which we refer to as the “Planck cold cloud” or PCC) in the southern outskirts of the galaxy where star formation activity is very low and largely confined to one location. We decompose the cloud into structures using a dendrogram and apply an identical analysis to matched-resolution cubes of the 30 Doradus molecular cloud (located near intense star formation) for comparison. Structures in the PCC exhibit roughly 10 times lower surface density and five times lower velocity dispersion than comparably sized structures in 30 Dor, underscoring the non-universality of molecular cloud properties. In both clouds, structures with relatively higher surface density lie closer to simple virial equilibrium, whereas lower surface-density structures tend to exhibit supervirial line widths. In the PCC, relatively high line widths are found in the vicinity of an infrared source whose properties are consistent with a luminous young stellar object. More generally, we find that the smallest resolved structures (“leaves”) of the dendrogram span close to the full range of line widths observed across all scales. As a result, while the bulk of the kinetic energy is found on the largest scales, the small-scale energetics tend to be dominated by only a few structures, leading to substantial scatter in observed size-line-width relationships.

ESTIMATION OF PHYSICAL PROPERTIES AND CHEMICAL REACTIVITY PARAMETERS OF ORGANIC COMPOUNDS

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 properties of steroids involved in their effects on the biophysical state of membranes.

PubMed

Wenz, Jorge J

2015-10-01

The activity of steroids on membranes was studied in relation to their ordering, rigidifying, condensing and/or raft promoting ability. The structures of 82 steroids were modeled by a semi-empirical procedure (AM1) and 245 molecular descriptors were next computed on the optimized energy conformations. Principal component analysis, mean contrasting and logistic regression were used to correlate the molecular properties with 212 cases of documented activities. It was possible to group steroids based on their properties and activities, indicating that steroids having similar molecular properties have similar activities on membranes. Steroids having high values of area, partition coefficient, volume, number of rotatable bonds, molar refractivity, polarizability or mass displayed ordering, rigidifying, condensing and/or raft promoting activity on membranes higher than those steroids having low values in such molecular properties. After a variable selection procedure circumventing correlation problems among descriptors, area and log P were found as the most relevant properties in governing and predicting the activity of steroids on membranes. A logistic regression model as a function of the area and log P of the steroids is proposed, which is able to predict correctly 92.5% of the cases. A rationale of the findings is discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Engineering controllable bidirectional molecular motors based on myosin

PubMed Central

Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

2012-01-01

Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells1, and have potential applications in molecular detection and diagnostic devices2,3. Engineering molecular motors with dynamically controllable properties will allow selective perturbation of mechanical processes in living cells, and yield optimized device components for complex tasks such as molecular sorting and directed assembly3. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions4,5 and other signals6. Here we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies7–11 and guided by a structural model12 for the redirected power stroke of myosin VI, we constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our general strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should enable spatiotemporal control over a range of motor properties including processivity, stride size13, and branchpoint turning14. PMID:22343382

Engineering controllable bidirectional molecular motors based on myosin

NASA Astrophysics Data System (ADS)

Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

2012-04-01

Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.

Evaluation of the Molecular Structural Parameters of Normal Rice Starch and Their Relationships with Its Thermal and Digestion Properties.

PubMed

Lin, Lingshang; Zhang, Qing; Zhang, Long; Wei, Cunxu

2017-09-12

The molecular structural parameters of six normal rice starches with different amylose contents were investigated through their iodine absorption spectra and gel permeation chromatography of fully branched and debranched starches. The thermal and digestion properties of starches were also determined and their relationships with molecular structural parameters were analyzed. Results showed that the molecular structural parameters of maximum absorption wavelength, blue value (BV), optical density 620 nm/550 nm (OD 620/550), amylose, intermediate component, and amylopectin, including its short branch-chains, long branch-chains, and branching degree, had high correlation in different determining methods. The intermediate component of starch was significantly positively related to amylose and negatively related to amylopectin, and the amylopectin branching degree was significantly positively related to amylopectin content and negatively related to amylose content. The gelatinization temperatures and enthalpy of native starch were significantly positively related to BV, OD 620/550, and amylose content and negatively related to amylopectin short branch-chains. The gelatinization temperatures and enthalpy of retrograded starch were significantly negatively related to amylopectin branching degree. The digestions of gelatinized and retrograded starches were significantly negatively related to the BV, OD 620/550, amylose, and intermediate component and positively related to amylopectin and its short branch-chains and branching degree.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Mechanism for starch granule ghost formation deduced from structural and enzyme digestion properties.

PubMed

Zhang, Bin; Dhital, Sushil; Flanagan, Bernadine M; Gidley, Michael J

2014-01-22

After heating in excess water under little or no shear, starch granules do not dissolve completely but persist as highly swollen fragile forms, commonly termed granule "ghosts". The macromolecular architecture of these ghosts has not been defined, despite their importance in determining characteristic properties of starches. In this study, amylase digestion of isolated granule ghosts from maize and potato starches is used as a probe to study the mechanism of ghost formation, through microstructural, mesoscopic, and molecular scale analyses of structure before and after digestion. Digestion profiles showed that neither integral nor surface proteins/lipids were crucial for control of either ghost digestion or integrity. On the basis of the molecular composition and conformation of enzyme-resistant fractions, it was concluded that the condensed polymeric surface structure of ghost particles is mainly composed of nonordered but entangled amylopectin (and some amylose) molecules, with limited reinforcement through partially ordered enzyme-resistant structures based on amylose (for maize starch; V-type order) or amylopectin (for potato starch; B-type order). The high level of branching and large molecular size of amylopectin is proposed to be the origin for the unusual stability of a solid structure based primarily on temporary entanglements.

Methoxydiphenylamine-substituted fluorene derivatives as hole transporting materials: role of molecular interaction on device photovoltaic performance.

PubMed

Tiazkis, Robertas; Paek, Sanghyun; Daskeviciene, Maryte; Malinauskas, Tadas; Saliba, Michael; Nekrasovas, Jonas; Jankauskas, Vygintas; Ahmad, Shahzada; Getautis, Vytautas; Khaja Nazeeruddin, Mohammad

2017-03-10

The molecular structure of the hole transporting material (HTM) play an important role in hole extraction in a perovskite solar cells. It has a significant influence on the molecular planarity, energy level, and charge transport properties. Understanding the relationship between the chemical structure of the HTM's and perovskite solar cells (PSCs) performance is crucial for the continued development of the efficient organic charge transporting materials. Using molecular engineering approach we have constructed a series of the hole transporting materials with strategically placed aliphatic substituents to investigate the relationship between the chemical structure of the HTMs and the photovoltaic performance. PSCs employing the investigated HTMs demonstrate power conversion efficiency values in the range of 9% to 16.8% highlighting the importance of the optimal molecular structure. An inappropriately placed side group could compromise the device performance. Due to the ease of synthesis and moieties employed in its construction, it offers a wide range of possible structural modifications. This class of molecules has a great potential for structural optimization in order to realize simple and efficient small molecule based HTMs for perovskite solar cells application.

Improved actuation strain of PDMS-based DEA materials chemically modified with softening agents

NASA Astrophysics Data System (ADS)

Biedermann, Miriam; Blümke, Martin; Wegener, Michael; Krüger, Hartmut

2015-04-01

Dielectric elastomer actuators (DEAs) are smart materials that gained much in interest particularly in recent years. One active field of research is the improvement of their properties by modification of their structural framework. The object of this work is to improve the actuation properties of polydimethylsiloxane (PDMS)-based DEAs by covalent incorporation of mono-vinyl-terminated low-molecular PDMS chains into the PDMS network. These low-molecular units act as a kind of softener within the PDMS network. The loose chain ends interfere with the network formation and lower the network's density. PDMS films with up to 50wt% of low-molecular PDMS additives were manufactured and the chemical, mechanical, electrical, and electromechanical properties of these novel materials were investigated.

Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations

NASA Astrophysics Data System (ADS)

Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo

2010-11-01

In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.

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

PubMed

Ratkova, Ekaterina L; Fedorov, Maxim V

2011-12-28

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

The Effect of Molecular Weight on the Composite Properties of Cured Phenylethynyl Terminated Imide Oligomers

NASA Technical Reports Server (NTRS)

Smith, J. G., Jr.; Connell, J. W.; Hergenrother, P. M.

1997-01-01

As part of a program to develop high temperature/high performance structural resins for aeronautical applications, imide oligomers containing terminal phenylethynyl groups with calculated number average molecular weights of 1250, 2500 and 5000 g/mol were prepared, characterized, and evaluated as adhesives and composite matrix resins. The goal of this work was to develop resin systems that are processable using conventional processing equipment into void free composites that exhibit high mechanical properties with long term high temperature durability, and are not affected by exposure to common aircraft fluids. The imide oligomers containing terminal phenylethynyl groups were fabricated into titanium adhesive specimens and IM-7 carbon fiber laminates under 0.1 - 1.4 MPa for 1 hr at 350-371 C. The lower molecular weight oligomers exhibited higher cured Tg, better processability, and better retention of mechanical properties at elevated temperature without significantly sacrificing toughness or damage tolerance than the higher molecular weight oligomer. The neat resin, adhesive and composite properties of the cured polymers will be presented.

Structure and dynamics of the peptide strand KRFK from the thrombospondin TSP-1 in water.

PubMed

Taleb Bendiab, W; Benomrane, B; Bounaceur, B; Dauchez, M; Krallafa, A M

2018-02-14

Theoretical investigations of a solute in liquid water at normal temperature and pressure can be performed at different levels of theory. Static quantum calculations as well as classical and ab initio molecular dynamics are used to completely explore the conformational space for large solvated molecular systems. In the classical approach, it is essential to describe all of the interactions of the solute and the solvent in detail. Water molecules are very often described as rigid bodies when the most commonly used interaction potentials, such as the SPCE and the TIP4P models, are employed. Recently, a physical model based upon a cluster of rigid water molecules with a tetrahedral architecture (AB 4 ) was proposed that describes liquid water as a mixture of both TIP4P and SPCE molecular species that occur in the proportions implied by the tetrahedral architecture (one central molecule versus four outer molecules; i.e., 20% TIP4P versus 80% SPCE molecules). In this work, theoretical spectroscopic data for a peptide strand were correlated with the structural properties of the peptide strand solvated in water, based on data calculated using different theoretical approaches and physical models. We focused on a particular peptide strand, KRFK (lysine-arginine-phenylalanine-lysine), found in the thrombospondin TSP-1, due to its interesting properties. As the activity and electronic structure of this system is strongly linked to its structure, we correlated its structure with charge-density maps obtained using different semi-empirical charge Q eq equations. The structural and thermodynamic properties obtained from classical simulations were correlated with ab initio molecular dynamics (AIMD) data. Structural changes in the peptide strand were rationalized in terms of the motions of atoms and groups of atoms. To achieve this, conformational changes were investigated using calculated infrared spectra for the peptide in the gas phase and in water solvent. The calculated AIMD infrared spectrum for the peptide was correlated with static quantum calculations of the molecular system based on a harmonic approach as well as the VDOS (vibrational density of states) spectra obtained using various classical solvent models (SPCE, TIP4P, and AB 4 ) and charge maps.

COMPARATIVE STUDY OF THREE FUNDAMENTAL ORGANIC COMPOUNDS OF CHAIN STRUCTURE OF THREE RINGS An approach based in the molecular descriptors of the DFT (Density Functional Theory)

NASA Astrophysics Data System (ADS)

Leon, Neira B. Oscar; Fabio, Mejía Elio; Elizabeth, y. Rincón B.

2008-04-01

The organic molecules of a chain structure containing phenyl, oxazole and oxadiazole rings are used in different combinations as active media for tunable lasers. From this viewpoint, we focused in the theoretical study of organic compounds of three rings, which have similar optical properties (fluorescence and laser properties). The main goal of this study is to compare the electronic structure through the analysis of molecular global descriptors defined in the DFT framework of2-[2-X-phenyl]-5-phenyl-1,3-Oxazole, 2-[2-X-phenyl]-5-phenyl-1,3,4-Oxadiazole, and 2-[2-X-phenyl]-5-phenyl-furane with X = H, F and Cl. The basis set used was 6-31G+(d).

The effect of self-sorting and co-assembly on the mechanical properties of low molecular weight hydrogels

NASA Astrophysics Data System (ADS)

Colquhoun, Catherine; Draper, Emily R.; Eden, Edward G. B.; Cattoz, Beatrice N.; Morris, Kyle L.; Chen, Lin; McDonald, Tom O.; Terry, Ann E.; Griffiths, Peter C.; Serpell, Louise C.; Adams, Dave J.

2014-10-01

Self-sorting in low molecular weight hydrogels can be achieved using a pH triggered approach. We show here that this method can be used to prepare gels with different types of mechanical properties. Cooperative, disruptive or orthogonal assembled systems can be produced. Gels with interesting behaviour can be also prepared, for example self-sorted gels where delayed switch-on of gelation occurs. By careful choice of gelator, co-assembled structures can also be generated, which leads to synergistic strengthening of the mechanical properties.Self-sorting in low molecular weight hydrogels can be achieved using a pH triggered approach. We show here that this method can be used to prepare gels with different types of mechanical properties. Cooperative, disruptive or orthogonal assembled systems can be produced. Gels with interesting behaviour can be also prepared, for example self-sorted gels where delayed switch-on of gelation occurs. By careful choice of gelator, co-assembled structures can also be generated, which leads to synergistic strengthening of the mechanical properties. Electronic supplementary information (ESI) available: Full experimental and synthetic details for the dipeptides, full experimental descriptions, further NMR, single crystal diffraction data, fXRD data and SANS data. See DOI: 10.1039/c4nr04039b

Synthesis, electronic structure, molecular packing/morphology evolution, and carrier mobilities of pure oligo-/poly(alkylthiophenes).

PubMed

Zhang, Lei; Colella, Nicholas S; Liu, Feng; Trahan, Stephan; Baral, Jayanta K; Winter, H Henning; Mannsfeld, Stefan C B; Briseno, Alejandro L

2013-01-16

Monodispersed conjugated oligothiophenes are receiving attention in fundamental and applied science due to their interesting optical, optoelectronic, and charge transport properties. These "low molecular weight" polymers serve as model structures for the corresponding polymer analogues, which are inherently polydispersed. Here we report the synthesis, electronic structure, molecular packing/morphology, and charge transport properties of monodispersed oligothiophenes with up to six didodecylquaterthiophene (DDQT) building block repeat units (i.e., 24 thiophene units). At the point where the effective conjugation length is reached, the electronic structure showed convergence behavior to the corresponding polymer, poly(3,3"-didodecyl-quaterthiophene) (PQT-12). X-ray crystal structure analysis of the dimer (DDQT-2) showed that terminal thiophenes exhibit syn-conformations, similar to the terminal syn-conformations observed in the trimer (DDQT-3). The dimer also exhibits a rare bending of the terminal alkyl side chains in order to prevent steric hindrance with neighboring hydrogens attached to core thiophenes. Grazing incidence X-ray scattering measurements revealed a morphology evolution from small molecule-like packing to polymer-like packing in thin films, with a morphology transition occurring near the effective conjugation length. Charge transport measurements showed a mobility increase with decreasing chain length. We correlated the molecular packing and morphology to charge transport and determined that carrier mobilities are most sensitive to crystallinity and crystal grain misorientation. This indicates that molecular weight is not a decisive factor for improved carrier mobility in the low molecular weight region, but rather the degree in crystallinity and in-plane crystal orientation. These results represent a fundamental advancement in understanding the relationship between conjugation length and carrier mobilities in oligothiophene semiconductors.

An Insilico Design of Nanoclay Based Nanocomposites and Scaffolds in Bone Tissue Engineering

NASA Astrophysics Data System (ADS)

Sharma, Anurag

A multiscale in silico approach to design polymer nanocomposites and scaffolds for bone tissue engineering applications is described in this study. This study focuses on the role of biomaterials design and selection, structural integrity and mechanical properties evolution during degradation and tissue regeneration in the successful design of polymer nanocomposite scaffolds. Polymer nanocomposite scaffolds are synthesized using aminoacid modified montmorillonite nanoclay with biomineralized hydroxyapatite and polycaprolactone (PCL/in situ HAPclay). Representative molecular models of polymer nanocomposite system are systematically developed using molecular dynamics (MD) technique and successfully validated using material characterization techniques. The constant force steered molecular dynamics (fSMD) simulation results indicate a two-phase nanomechanical behavior of the polymer nanocomposite. The MD and fSMD simulations results provide quantitative contributions of molecular interactions between different constituents of representative models and their effect on nanomechanical responses of nanoclay based polymer nanocomposite system. A finite element (FE) model of PCL/in situ HAPclay scaffold is built using micro-computed tomography images and bridging the nanomechanical properties obtained from fSMD simulations into the FE model. A new reduction factor, K is introduced into modeling results to consider the effect of wall porosity of the polymer scaffold. The effect of accelerated degradation under alkaline conditions and human osteoblast cells culture on the evolution of mechanical properties of scaffolds are studied and the damage mechanics based analytical models are developed. Finally, the novel multiscale models are developed that incorporate the complex molecular and microstructural properties, mechanical properties at nanoscale and structural levels and mechanical properties evolution during degradation and tissue formation in the polymer nanocomposite scaffold. Overall, this study provides a leap into methodologies for in silico design of biomaterials for bone tissue engineering applications. Furthermore, as a part of this work, a molecular dynamics study of rice DNA in the presence of single walled carbon nanotube is carried out to understand the role played by molecular interactions in the conformation changes of rice DNA. The simulations results showed wrapping of DNA onto SWCNT, breaking and forming of hydrogen bonds due to unzipping of Watson-Crick (WC) nucleobase pairs and forming of new non-WC nucleobase pairs in DNA.

Ferromagnetism and the electronic band structure in (Ga,Mn)(Bi,As) epitaxial layers

NASA Astrophysics Data System (ADS)

Yastrubchak, O.; Sadowski, J.; Gluba, L.; Domagala, J. Z.; Rawski, M.; Żuk, J.; Kulik, M.; Andrearczyk, T.; Wosinski, T.

2014-08-01

Impact of Bi incorporation into (Ga,Mn)As layers on their electronic- and band-structures as well as their magnetic and structural properties has been studied. Homogenous (Ga,Mn)(Bi,As) layers of high structural perfection have been grown by the low-temperature molecular-beam epitaxy technique. Post-growth annealing treatment of the layers results in an improvement of their structural and magnetic properties and an increase in the hole concentration in the layers. The modulation photoreflectance spectroscopy results are consistent with the valence-band model of hole-mediated ferromagnetism in the layers. This material combines the properties of (Ga,Mn)As and Ga(Bi,As) ternary compounds and offers the possibility of tuning its electrical and magnetic properties by controlling the alloy composition.

The TiPS/TINS lecture: the molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-08-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.

The TINS/TiPS Lecture. The molecular biology of mammalian glutamate receptor channels.

PubMed

Seeburg, P H

1993-09-01

In native brain membranes the principal excitatory neurotransmitter L-glutamate activates cation-conducting channels with distinct biophysical and pharmacological properties. Molecular cloning has revealed the existence of 16 channel subunits that can assemble in homomeric or heteromeric configurations in vitro to form receptor channels with disparate functional properties. This review describes the different channel types obtained by recombinant means and the genetic mechanisms controlling the expression of functionally important channel structures.

FT-IR, FT-Raman and NMR characterization of 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate and investigation of its reactive and optoelectronic properties by molecular dynamics simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Menon, Vidya V.; Fazal, Edakot; Mary, Y. Sheena; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Nagarajan, Subban; Van Alsenoy, C.

2017-01-01

The FT-IR and FT-Raman spectra of the synthesized compound, 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate is recorded and analyzed. Optimized molecular structure, wave numbers, corresponding assignments regarding 2-isopropyl-5-methylcyclohexyl quinoline-2-carboxylate has become screened tentatively as well as hypothetically using Gaussian09 program package. Natural bonding orbital assessment has been completed with a reason to clarify charge transfer or conjugative interaction, the intra-molecular re-hybridization and delocalization of electron density within the molecule. The NMR spectral assessment had been made choosing structure property relationship by chemical shifts along with the magnetic shielding effects regarding the title compound. The first and second hyperpolarizabilities were calculated. The calculated first order hyperpolarizability is commensurate with the documented worth of very similar derivatives and could be an interesting object for more experiments on nonlinear optics. Local reactivity properties have been investigated using average local ionization energies and Fukui functions. Investigation of optoelectronic properties encompassed calculations of reorganization energies and hopping rates of charge carriers within the framework of Marcus semi-empiric approach. The docked ligand title compound forms a stable complex with CDK inhibitors and gives a binding affinity value of -9.7 kcal/mol and molecular docking results suggest that the compound might exhibit inhibitory activity against CDK inhibitors.

Updating CMAQ secondary organic aerosol properties relevant for aerosol water interactions

EPA Science Inventory

Properties of secondary organic aerosol (SOA) compounds in CMAQ are updated with state-of-the-science estimates from structure activity relationships to provide consistency among volatility, molecular weight, degree of oxygenation, and solubility/hygroscopicity. These updated pro...

Conjugated Organosilicon Materials for Organic Electronics and Photonics

NASA Astrophysics Data System (ADS)

Ponomarenko, Sergei A.; Kirchmeyer, Stephan

In this chapter different types of conjugated organosilicon materials possessing luminescent and/or semiconducting properties will be described. Such macromolecules have various topologies and molecular structures: linear, branched and hyperbranched oligomers, polymers, and dendrimers. Specific synthetic approaches to access these structures will be discussed. Special attention is devoted to the role of silicon in these structures and its influence on their optical and electrical properties, leading to their potential application in the emerging areas of organic and hybrid electronics.

Examining the Chemical and Structural Properties that Influence the Sensitivity of Energetic Nitrate Esters

DOE PAGES

Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.; ...

2018-03-09

The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less

Examining the Chemical and Structural Properties that Influence the Sensitivity of Energetic Nitrate Esters

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

Manner, Virginia W.; Cawkwell, Marc; Kober, Edward M.

The sensitivity of explosives is controlled by factors that span from intrinsic chemical reactivity and chemical intramolecular effects to mesoscale structure and defects, and has been a topic of extensive study for over 50 years. Due to these complex competing chemical and physical elements, a unifying relationship between molecular framework, crystal structure, and sensitivity has yet to be developed. In order to move towards this goal, ideally experimental studies should be performed on systems with small, systematic structural modifications, with modeling utilized to interpret experimental results. Pentaerythritol tetranitrate (PETN) is a common nitrate ester explosive that has been widely studiedmore » due to its use in military and commercial explosives. We have synthesized PETN derivatives with modified sensitivity characteristics by substituting the CCH 2ONO 2 moiety with other substituents, including CH, CNH 2, CNH3X, CCH 3, and PO. We relate the handling sensitivity properties of each PETN derivative to its structural properties, and discuss the potential roles of thermodynamic properties such as heat capacity and heat of formation, thermal stability, crystal structure, compressibility, and inter- and intramolecular hydrogen bonding on impact sensitivity. Reactive molecular dynamics (MD) simulations of the C/H/N/O-based PETN-derivatives have been performed under cook-off conditions that mimic those accessed in impact tests. These simulations infer how changes in chemistry affect the subsequent decomposition pathways.« less

3-D Structure of Molecules of Biological Significance

ERIC Educational Resources Information Center

Bennett, Alice S.; Schwenk, Karl

1974-01-01

Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

Boiling points of halogenated aliphatic compounds: a quantitative structure-property relationship for prediction and validation.

PubMed

Oberg, Tomas

2004-01-01

Halogenated aliphatic compounds have many technical uses, but substances within this group are also ubiquitous environmental pollutants that can affect the ozone layer and contribute to global warming. The establishment of quantitative structure-property relationships is of interest not only to fill in gaps in the available database but also to validate experimental data already acquired. The three-dimensional structures of 240 compounds were modeled with molecular mechanics prior to the generation of empirical descriptors. Two bilinear projection methods, principal component analysis (PCA) and partial-least-squares regression (PLSR), were used to identify outliers. PLSR was subsequently used to build a multivariate calibration model by extracting the latent variables that describe most of the covariation between the molecular structure and the boiling point. Boiling points were also estimated with an extension of the group contribution method of Stein and Brown.

Nanoscale studies link amyloid maturity with polyglutamine diseases onset

NASA Astrophysics Data System (ADS)

Ruggeri, F. S.; Vieweg, S.; Cendrowska, U.; Longo, G.; Chiki, A.; Lashuel, H. A.; Dietler, G.

2016-08-01

The presence of expanded poly-glutamine (polyQ) repeats in proteins is directly linked to the pathogenesis of several neurodegenerative diseases, including Huntington’s disease. However, the molecular and structural basis underlying the increased toxicity of aggregates formed by proteins containing expanded polyQ repeats remain poorly understood, in part due to the size and morphological heterogeneity of the aggregates they form in vitro. To address this knowledge gap and technical limitations, we investigated the structural, mechanical and morphological properties of fibrillar aggregates at the single molecule and nanometer scale using the first exon of the Huntingtin protein as a model system (Exon1). Our findings demonstrate a direct correlation of the morphological and mechanical properties of Exon1 aggregates with their structural organization at the single aggregate and nanometric scale and provide novel insights into the molecular and structural basis of Huntingtin Exon1 aggregation and toxicity.

Anti-inflammatory drugs and prediction of new structures by comparative analysis.

PubMed

Bartzatt, Ronald

2012-01-01

Nonsteroidal anti-inflammatory drugs (NSAIDs) are a group of agents important for their analgesic, anti-inflammatory, and antipyretic properties. This study presents several approaches to predict and elucidate new molecular structures of NSAIDs based on 36 known and proven anti-inflammatory compounds. Based on 36 known NSAIDs the mean value of Log P is found to be 3.338 (standard deviation= 1.237), mean value of polar surface area is 63.176 Angstroms2 (standard deviation = 20.951 A2), and the mean value of molecular weight is 292.665 (standard deviation = 55.627). Nine molecular properties are determined for these 36 NSAID agents, including Log P, number of -OH and -NHn, violations of Rule of 5, number of rotatable bonds, and number of oxygens and nitrogens. Statistical analysis of these nine molecular properties provides numerical parameters to conform to in the design of novel NSAID drug candidates. Multiple regression analysis is accomplished using these properties of 36 agents followed with examples of predicted molecular weight based on minimum and maximum property values. Hierarchical cluster analysis indicated that licofelone, tolfenamic acid, meclofenamic acid, droxicam, and aspirin are substantially distinct from all remaining NSAIDs. Analysis of similarity (ANOSIM) produced R = 0.4947, which indicates low to moderate level of dissimilarity between these 36 NSAIDs. Non-hierarchical K-means cluster analysis separated the 36 NSAIDs into four groups having members of greatest similarity. Likewise, discriminant analysis divided the 36 agents into two groups indicating the greatest level of distinction (discrimination) based on nine properties. These two multivariate methods together provide investigators a means to compare and elucidate novel drug designs to 36 proven compounds and ascertain to which of those are most analogous in pharmacodynamics. In addition, artificial neural network modeling is demonstrated as an approach to predict numerous molecular properties of new drug designs that is based on neural training from 36 proven NSAIDs. Comprehensive and effective approaches are presented in this study for the design of new NSAID type agents which are so very important for inhibition of COX-2 and COX-1 isoenzymes.

Lattice enumeration for inverse molecular design using the signature descriptor.

PubMed

Martin, Shawn

2012-07-23

We describe an inverse quantitative structure-activity relationship (QSAR) framework developed for the design of molecular structures with desired properties. This framework uses chemical fragments encoded with a molecular descriptor known as a signature. It solves a system of linear constrained Diophantine equations to reorganize the fragments into novel molecular structures. The method has been previously applied to problems in drug and materials design but has inherent computational limitations due to the necessity of solving the Diophantine constraints. We propose a new approach to overcome these limitations using the Fincke-Pohst algorithm for lattice enumeration. We benchmark the new approach against previous results on LFA-1/ICAM-1 inhibitory peptides, linear homopolymers, and hydrofluoroether foam blowing agents. Software implementing the new approach is available at www.cs.otago.ac.nz/homepages/smartin.

Ternary AlGaN Alloys with High Al Content and Enhanced Compositional Homogeneity Grown by Plasma-Assisted Molecular Beam Epitaxy

NASA Astrophysics Data System (ADS)

Fellmann, Vincent; Jaffrennou, Périne; Sam-Giao, Diane; Gayral, Bruno; Lorenz, Katharina; Alves, Eduardo; Daudin, Bruno

2011-03-01

We have studied the influence of III/N flux ratio and growth temperature on structural and optical properties of high Al-content, around 50-60%, AlGaN alloy layers grown by plasma-assisted molecular beam epitaxy. In a first part, based on structural analysis by Rutherford Backscattering Spectroscopy, we establish that a III/N flux ratio slightly above 1 produces layers with low amount of structural defects. In a second part, we study the effect of growth temperature on structural and optical properties of layers grown with previously determined optimal III/N flux ratio. We find that optimal growth temperatures for Al0.50Ga0.50N layers with compositional homogeneity related with narrow UV photoluminescence properties are in the low temperature range for growing GaN layers, i.e., 650-680 °C. We propose that lowering Ga adatom diffusion on the surface favors random incorporation of both Ga and Al adatoms on wurtzite crystallographic sites leading to the formation of an homogeneous alloy.

DFT calculations on spectroscopic and structural properties of a NLO chromophore

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

2016-03-01

The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis-Diazacyclic Libraries

PubMed Central

López-Vallejo, Fabian; Nefzi, Adel; Bender, Andreas; Owen, John R.; Nabney, Ian T.; Houghten, Richard A.; Medina-Franco, Jose L.

2011-01-01

Combinatorial libraries continue to play a key role in drug discovery. To increase structural diversity, several experimental methods have been developed. However, limited efforts have been performed so far to quantify the diversity of the broadly used diversity-oriented synthetic (DOS) libraries. Herein we report a comprehensive characterization of 15 bis-diazacyclic combinatorial libraries obtained through libraries from libraries, which is a DOS approach. Using MACCS keys, radial and different pharmacophoric fingerprints as well as six molecular properties, it was demonstrated the increased structural and property diversity of the libraries from libraries over the individual libraries. Comparison of the libraries to existing drugs, NCI Diversity and the Molecular Libraries Small Molecule Repository revealed the structural uniqueness of the combinatorial libraries (mean similarity < 0.5 for any fingerprint representation). In particular, bis-cyclic thiourea libraries were the most structurally dissimilar to drugs retaining drug-like character in property space. This study represents the first comprehensive quantification of the diversity of libraries from libraries providing a solid quantitative approach to compare and contrast the diversity of DOS libraries with existing drugs or any other compound collection. PMID:21294850

Molecular dynamics calculation on structures, stabilities, mechanical properties, and energy density of CL-20/FOX-7 cocrystal explosives.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-11-30

In this article, different CL-20/FOX-7 cocrystal models were established by the substitution method based on the molar ratios of CL-20:FOX-7. The structures and comprehensive properties, including mechanical properties, stabilities, and energy density, of different cocrystal models were obtained and compared with each other. The main aim was to estimate the influence of molar ratios on properties of cocrystal explosives. The molecular dynamics (MD) simulation results show that the cocrystal model with molar ratio 1:1 has the best mechanical properties and highest binding energy, so the CL-20/FOX-7 cocrystal model is more likely to form in 1:1 M ratio. The detonation parameters show that the cocrystal explosive exhibited preferable energy density and excellent detonation performance. In a word, the 1:1 cocrystal model has the best comprehensive properties, is very promising, and worth more theoretical investigations and experimental tests. This paper gives some original theories to better understand the cocrystal mechanism and provides some helpful guidance and useful instructions to help design CL-20 cocrystal explosives.

Modeling adsorption properties of structurally deformed metal–organic frameworks using structure–property map

PubMed Central

Lim, Dae-Woon; Kim, Sungjune; Harale, Aadesh; Yoon, Minyoung; Suh, Myunghyun Paik; Kim, Jihan

2017-01-01

Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure–property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure–property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure–property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure–property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost. PMID:28696307

Keeping the ball rolling: fullerene-like molecular clusters.

PubMed

Kong, Xiang-Jian; Long, La-Sheng; Zheng, Zhiping; Huang, Rong-Bin; Zheng, Lan-Sun

2010-02-16

The discovery of fullerenes in 1985 opened a new chapter in the chemistry of highly symmetric molecules. Fullerene-like metal clusters, characterized by (multi)shell-like structures, are one rapidly developing class of molecules that share this shape. In addition to creating aesthetically pleasing molecular structures, the ordered arrangement of metal atoms within such frameworks provides the opportunity to develop materials with properties not readily achieved in corresponding mononuclear or lower-nuclearity complexes. In this Account, we survey the great variety of fullerene-like metal-containing clusters with an emphasis on their synthetic and structural chemistry, a first step in the discussion of this fascinating field of cluster chemistry. We group the compounds of interest into three categories based on the atomic composition of the cluster core: those with formal metal-metal bonding, those characterized by ligand participation, and those supported by polyoxometalate building blocks. The number of clusters in the first group, containing metal-metal bonds, is relatively small. However, because of the unique and complex bonding scenarios observed for some of these species, these metalloid clusters present a number of research questions with significant ramifications. Because these cores contain molecular clusters of precious metals at the nanoscale, they offer an opportunity to study chemical properties at size ranges from the molecular to nanoscale and to gain insights into the electronic structures and properties of nanomaterials of similar chemical compositions. Clusters of the second type, whose core structures are facilitated by ligand participation, could aid in the development of functional materials. Of particular interest are the magnetic clusters containing both transition and lanthanide elements. A series of such heterometallic clusters that we prepared demonstrates diverse magnetic properties including antiferromagnetism, ferrimagnetism, and ferromagnetism. Considering the diversity of their composition, their distinct electronic structures, and the disparate coordination behaviors of the different metal elements, these materials suggest abundant opportunities for designing multifunctional materials with varied structures. The third type of clusters that we discuss are based on polyoxometalates, in particular those containing pentagonal units. However, unlike in fullerene chemistry, which does not allow the use of discrete pentagonal building blocks, the metal oxide-based pentagonal units can be used as fundamental building blocks for constructing various Keplerate structures. These structures also have a variety of functions, including intriguing magnetic properties in some cases. Coupled with different linking groups, such pentagonal units can be used for the assembly of a large number of spherical molecules whose properties can be tuned and optimized. Although this Account focuses on the topological aspects of fullerene-like metal clusters, we hope that this topical review will stimulate more efforts in the exploratory synthesis of new fullerene-like clusters. More importantly, we hope that further study of the bonding interactions and properties of these molecules will lead to the development of new functional materials.

PREDICTION OF MOLECULAR PROPERTIES WITH MID-INFRARED SPECTRA AND INTERFEROGRAMS

EPA Science Inventory

We have built infrared spectroscopy-based partial least squares (PLS) models for molecular polarizabilities using a 97 member training set and a 59 member independent prediction set. These 156 compounds span a very wide range of chemical structure. Our goal was to use this well...

A Molecular Dynamics Study of Single-Walled Carbon Nanotubes (SWCNTs) Dispersed in Bile Salt Surfactants

NASA Astrophysics Data System (ADS)

Phelan, Frederick, Jr.; Sun, Huai

2014-03-01

Single-walled carbon nanotubes (SWNCTs) are materials with structural, electronic and optical properties that make them attractive for a myriad of advanced technology applications. A practical barrier to their use is that SWCNT synthesis techniques produce heterogeneous mixtures of varying lengths and chirality, whereas applications generally require tubes with narrow size distributions and individual type. Most separation techniques currently in use to obtain monodisperse tube fractions rely on dispersion of these materials in aqueous solution using surfactants. The dispersion process results in a mixture of colloidal structures in which individual tubes are dispersed and contained in a surfactant shell. Understanding the structure and properties of the SWCNT-surfactant complex at the molecular level, and how this is affected by chirality, is key to understanding and improving separations processes. In this study, we use molecular dynamics (MD) simulations to study the structure and properties of SWCNT-surfactant colloidal complexes. We tested a number of methods and protocols in order to build an accurate model for simulating SWCNT systems for a variety of bile salt surfactants as well as anionic co-surfactants, components that are widely used and important in experimental separation studies at NIST. The custom force field parameters used here will be stored in WebFF, a Web-hosted smart force-field repository for polymeric and organic materials being developed at NIST for the Materials Genome Initiative.

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

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

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations.

PubMed

Torchi, Andrea; Bochicchio, Davide; Pavan, Giovanni M

2018-04-12

The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.

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

PubMed

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

2018-04-26

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

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Protein based Block Copolymers

PubMed Central

Rabotyagova, Olena S.; Cebe, Peggy; Kaplan, David L.

2011-01-01

Advances in genetic engineering have led to the synthesis of protein-based block copolymers with control of chemistry and molecular weight, resulting in unique physical and biological properties. The benefits from incorporating peptide blocks into copolymer designs arise from the fundamental properties of proteins to adopt ordered conformations and to undergo self-assembly, providing control over structure formation at various length scales when compared to conventional block copolymers. This review covers the synthesis, structure, assembly, properties, and applications of protein-based block copolymers. PMID:21235251

Surfactant Effects on Structure and Mechanical Properties of Ultrahigh-Molecular-Weight Polyethylene/Layered Silicate Composites.

PubMed

Nikiforov, Leonid A; Okhlopkova, Tatinana A; Kapitonova, Iullia V; Sleptsova, Sardana A; Okhlopkova, Aitalina A; Shim, Ee Le; Cho, Jin-Ho

2017-12-05

In this study, the reinforcement of ultrahigh-molecular-weight polyethylene (UHMWPE) with biotite was investigated. The biotite filler was mechanically activated with different dry surfactants to improve its compatibility with UHMWPE and decrease agglomeration among biotite particles. Alkyldimethylbenzylammonium chloride (ADBAC) and cetyltrimethylammonium bromide (CTAB) were selected as cationic surfactants. The tensile strength of composites containing 1 wt % of CTAB-treated biotite was increased by 30% relative to those with untreated biotite, but was unchanged with ADBAC treatment of the same biotite content. The stereochemistry of the surfactant may be critical to the composite structure and mechanical properties of the material. The stereochemistry of CTAB was preferable to that of ADBAC in enhancing mechanical properties because the stereochemistry of ADBAC impedes favorable interactions with the biotite surface during mechanical activation.

High temperature arc-track resistant aerospace insulation

NASA Technical Reports Server (NTRS)

Dorogy, William

1994-01-01

The topics are presented in viewgraph form and include the following: high temperature aerospace insulation; Foster-Miller approach to develop a 300 C rated, arc-track resistant aerospace insulation; advantages and disadvantages of key structural features; summary goals and achievements of the phase 1 program; performance goals for selected materials; materials under evaluation; molecular structures of candidate polymers; candidate polymer properties; film properties; and a detailed program plan.

Fluorescent photochromes of diarylethene series: synthesis and properties

NASA Astrophysics Data System (ADS)

Shirinian, Valerii Z.; Lonshakov, D. V.; Lvov, A. G.; Krayushkin, Mikhail M.

2013-06-01

The research data in the field of fluorescent photochromic di(het)arylethenes published over the last decade are summarized. The characteristics of these compounds significant for their application in the design of molecular optical memory systems and photocontrolled switches are considered. The main types of diarylethenes and methods for their synthesis are described, and the correlations between structure and spectral properties, in particular, fluorescence characteristics are analyzed. Considerable attention is given to the means for endowing diarylethenes with fluorescence properties as one of the most promising methods for data readout from molecular information carriers. The bibliography includes 203 references.

The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap.

PubMed

Brown, Jeffrey W; Bullitt, Esther; Sriswasdi, Sira; Harper, Sandra; Speicher, David W; McKnight, C James

2015-06-01

The primary, secondary, and tertiary structures of spectrin are reasonably well defined, but the structural basis for the known dramatic molecular shape change, whereby the molecular length can increase three-fold, is not understood. In this study, we combine previously reported biochemical and high-resolution crystallographic data with structural mass spectroscopy and electron microscopic data to derive a detailed, experimentally-supported quaternary structure of the spectrin heterotetramer. In addition to explaining spectrin's physiological resting length of ~55-65 nm, our model provides a mechanism by which spectrin is able to undergo a seamless three-fold extension while remaining a linear filament, an experimentally observed property. According to the proposed model, spectrin's quaternary structure and mechanism of extension is similar to a Chinese Finger Trap: at shorter molecular lengths spectrin is a hollow cylinder that extends by increasing the pitch of each spectrin repeat, which decreases the internal diameter. We validated our model with electron microscopy, which demonstrated that, as predicted, spectrin is hollow at its biological resting length of ~55-65 nm. The model is further supported by zero-length chemical crosslink data indicative of an approximately 90 degree bend between adjacent spectrin repeats. The domain-domain interactions in our model are entirely consistent with those present in the prototypical linear antiparallel heterotetramer as well as recently reported inter-strand chemical crosslinks. The model is consistent with all known physical properties of spectrin, and upon full extension our Chinese Finger Trap Model reduces to the ~180-200 nm molecular model currently in common use.

QUANTIFYING OBSERVATIONAL PROJECTION EFFECTS USING MOLECULAR CLOUD SIMULATIONS

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

Beaumont, Christopher N.; Offner, Stella S.R.; Shetty, Rahul

2013-11-10

The physical properties of molecular clouds are often measured using spectral-line observations, which provide the only probes of the clouds' velocity structure. It is hard, though, to assess whether and to what extent intensity features in position-position-velocity (PPV) space correspond to 'real' density structures in position-position-position (PPP) space. In this paper, we create synthetic molecular cloud spectral-line maps of simulated molecular clouds, and present a new technique for measuring the reality of individual PPV structures. Using a dendrogram algorithm, we identify hierarchical structures in both PPP and PPV space. Our procedure projects density structures identified in PPP space into correspondingmore » intensity structures in PPV space and then measures the geometric overlap of the projected structures with structures identified from the synthetic observation. The fractional overlap between a PPP and PPV structure quantifies how well the synthetic observation recovers information about the three-dimensional structure. Applying this machinery to a set of synthetic observations of CO isotopes, we measure how well spectral-line measurements recover mass, size, velocity dispersion, and virial parameter for a simulated star-forming region. By disabling various steps of our analysis, we investigate how much opacity, chemistry, and gravity affect measurements of physical properties extracted from PPV cubes. For the simulations used here, which offer a decent, but not perfect, match to the properties of a star-forming region like Perseus, our results suggest that superposition induces a ∼40% uncertainty in masses, sizes, and velocity dispersions derived from {sup 13}CO (J = 1-0). As would be expected, superposition and confusion is worst in regions where the filling factor of emitting material is large. The virial parameter is most affected by superposition, such that estimates of the virial parameter derived from PPV and PPP information typically disagree by a factor of ∼2. This uncertainty makes it particularly difficult to judge whether gravitational or kinetic energy dominate a given region, since the majority of virial parameter measurements fall within a factor of two of the equipartition level α ∼ 2.« less

Highlights of 10th plasma chemistry meeting

NASA Technical Reports Server (NTRS)

Kitamura, K.; Hashimoto, H.; Hozumi, K.

1981-01-01

The chemical structure is given of a film formed by plasma polymerization from pyridine monomers. The film has a hydrophilic chemical structure, its molecular weight is 900, and the molecular system is C55H50N10O3. The electrical characteristics of a plasma polymerized film are described. The film has good insulating properties and was successfully applied as video disc coating. Etching resistance properties make it possible to use the film as a resist in etching. The characteristics of plasma polymer formed from monomers containing tetramethyltin are discussed. The polymer is in film form, displays good adhesiveness, is similar to UV film UV 35 in light absorption and is highly insulating.

Effect of nucleoside analogue antimetabolites on the structure of PEO–PPO–PEO micelles investigated by SANS

DOE PAGES

Han, Youngkyu; Zhang, Zhe; Smith, Gregory S.; ...

2017-04-19

In this work, the effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strengthmore » of the effect was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.« less

Effect of nucleoside analogue antimetabolites on the structure of PEO–PPO–PEO micelles investigated by SANS

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

Han, Youngkyu; Zhang, Zhe; Smith, Gregory S.

2017-01-01

The effect of three nucleoside analogue antimetabolites (5-fluorouracil, floxuridine, and gemcitabine) on the structure of Pluronic L62 copolymer micelles was investigated using small-angle neutron scattering. These antimetabolites used for cancer chemotherapy have analogous molecular structures but different molecular sizes and aqueous solubilities. It was found that the addition of the three antimetabolites slightly reduced the micellar size and aggregation number, and the micellar anisotropy. The added antimetabolites also changed the internal molecular distribution of the micelles as measured by the scattering length densities, resulting in enhanced hydration of the hydrophobic core region of the micelle. The strength of the effectmore » was found to correlate with the molecular properties of the model drugs, i.e. a larger molecular size and a higher aqueous solubility lead to enhanced hydration of the micellar core.« less

Molecular simulations and experimental studies of zeolites

NASA Astrophysics Data System (ADS)

Moloy, Eric C.

Zeolites are microporous aluminosilicate tetrahedral framework materials that have symmetric cages and channels with open-diameters between 0.2 and 2.0 nm. Zeolites are used extensively in the petrochemical industries for both their microporosity and their catalytic properties. The role of water is paramount to the formation, structure, and stability of these materials. Zeolites frequently have extra-framework cations, and as a result, are important ion-exchange materials. Zeolites also play important roles as molecular sieves and catalysts. For all that is known about zeolites, much remains a mystery. How, for example, can the well established metastability of these structures be explained? What is the role of water with respect to the formation, stabilization, and dynamical properties? This dissertation addresses these questions mainly from a modeling perspective, but also with some experimental work as well. The first discussion addresses a special class of zeolites: pure-silica zeolites. Experimental enthalpy of formation data are combined with molecular modeling to address zeolitic metastability. Molecular modeling is used to calculate internal surface areas, and a linear relationship between formation enthalpy and internal surface areas is clearly established, producing an internal surface energy of approximately 93 mJ/m2. Nitrate bearing sodalite and cancrinite have formed under the caustic chemical conditions of some nuclear waste processing centers in the United States. These phases have fouled expensive process equipment, and are the primary constituents of the resilient heels in the bottom of storage tanks. Molecular modeling, including molecular mechanics, molecular dynamics, and density functional theory, is used to simulate these materials with respect to structure and dynamical properties. Some new, very interesting results are extracted from the simulation of anhydrous Na6[Si6Al 6O24] sodalite---most importantly, the identification of two distinct oxygen sites (rather than one), and formation of a new supercell. New calorimetric measurements of enthalpy are used to examine the energetics of the hydrosodalite family of zeolites---specifically, formation enthalpies and hydration energies. Finally, force-field computational methods begin the examination of water in terms of energetics, structure, and radionuclide containment and diffusion.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

PubMed Central

Yamashita, Takefumi; Peng, Yuxing; Knight, Chris; Voth, Gregory A.

2012-01-01

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as “multistate”. These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations. PMID:25100924

M4Ag44(p-MBA)30 Molecular Nanoparticles

NASA Astrophysics Data System (ADS)

Conn, Brian E.

In recent years, molecular nanoparticles have attracted much attention due to their unique physical, optical, and electronic properties. The properties of molecular nanoparticles are shown to deviate from their larger bulk counterparts, due to quantum confinement effects and large surface-to-volume ratios. As the size of the nanoparticle shrinks to a cluster of metal atoms (<3 nm in diameter), there is an emergence of a HOMO-LUMO band gap, which is not present in transitional d-block metals. The HOMO-LUMO band gap gives rise to discrete electronic states, leading to new chemical and physical properties. Molecular nanoparticles have had a substantial impact across a diverse range of fields, including catalysis, sensing, photochemistry, optoelectronic, energy conversion, and medicine. Currently many of the synthetic procedures for molecular nanoparticles require low temperatures, long incubation times, multistep purification and hazardous reagents that produce low yields and polydisperse molecular nanoparticles with poor stability. Although silver has very desirable physical properties, good relative abundance and low cost, gold molecular nanoparticles have been widely favored owing to their proved stability and ease of use. Unlike gold, silver is notorious for its susceptibility to oxidation, i.e., tarnishing, which has limited the development of silver-based nanotechnologies. Despite two decades of synthetic efforts, silver molecular nanoparticles that are inert or have long-term stability have remained unrealized. Herein we report a simple synthetic protocol for producing ultrastable M4Ag44(p-MBA)30 nanoparticles as a single-sized molecular product and in exceptionally large quantities. The stability, purity, and yield are substantially better than other metal nanoparticles, including gold, due to several stabilization mechanisms. Also, reported are the structural and mechanical properties of extended crystalline solids of Na4Ag44(p-MBA)30 from large-scale quantum-mechanical simulations based on the atomically-precise X-ray measured structure. Calculations show that cohesion is derived from hydrogen bonds between bundled p-MBA ligands and that the superlattice's mechanical response to hydrostatic compression is characterized by a molecular-solid-like bulk modulus B0 = 16.7 GPa, exhibiting anomalous pressure softening and a compression-induced transition to a soft-solid phase. Such a transition involves ligand flexure, which causes gear-like correlated chiral rotation of the nanoparticles.

D2+ Molecular complex in non-uniform height quantum ribbon under crossed electric and magnetic fields

NASA Astrophysics Data System (ADS)

Suaza, Y. A.; Laroze, D.; Fulla, M. R.; Marín, J. H.

2018-05-01

The D2+ molecular complex fundamental properties in a uniform and multi-hilled semiconductor quantum ribbon under orthogonal electric and magnetic fields are theoretically studied. The energy structure is calculated by using adiabatic approximation combined with diagonalization procedure. The D2+ energy structure is more strongly controlled by the geometrical structural hills than the Coulomb interaction. The formation of vibrational and rotational states is discussed. Aharanov-Bohm oscillation patterns linked to rotational states as well as the D2+ molecular complex stability are highly sensitive to the number of hills while electric field breaks the electron rotational symmetry and removes the energy degeneration between low-lying states.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

PubMed

Pagano, Bruno; Jama, Abdullah; Martinez, Pierre; Akanho, Ester; Bui, Tam T T; Drake, Alex F; Fraternali, Franca; Nikolova, Penka V

2013-01-01

The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs) of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

SYVA: A program to analyze symmetry of molecules based on vector algebra

NASA Astrophysics Data System (ADS)

Gyevi-Nagy, László; Tasi, Gyula

2017-06-01

Symmetry is a useful concept in physics and chemistry. It can be used to find out some simple properties of a molecule or simplify complex calculations. In this paper a simple vector algebraic method is described to determine all symmetry elements of an arbitrary molecule. To carry out the symmetry analysis, a program has been written, which is also capable of generating the framework group of the molecule, revealing the symmetry properties of normal modes of vibration and symmetrizing the structure. To demonstrate the capabilities of the program, it is compared to other common widely used stand-alone symmetry analyzer (SYMMOL, Symmetrizer) and molecular modeling (NWChem, ORCA, MRCC) software. SYVA can generate input files for molecular modeling programs, e.g. Gaussian, using precisely symmetrized molecular structures. Possible applications are also demonstrated by integrating SYVA with the GAMESS and MRCC software.

The Developmental Regulator SEEDSTICK Controls Structural and Mechanical Properties of the Arabidopsis Seed Coat

PubMed Central

Beauzamy, Léna; Caporali, Elisabetta; Koroney, Abdoul-Salam

2016-01-01

Although many transcription factors involved in cell wall morphogenesis have been identified and studied, it is still unknown how genetic and molecular regulation of cell wall biosynthesis is integrated into developmental programs. We demonstrate by molecular genetic studies that SEEDSTICK (STK), a transcription factor controlling ovule and seed integument identity, directly regulates PMEI6 and other genes involved in the biogenesis of the cellulose-pectin matrix of the cell wall. Based on atomic force microscopy, immunocytochemistry, and chemical analyses, we propose that structural modifications of the cell wall matrix in the stk mutant contribute to defects in mucilage release and seed germination under water-stress conditions. Our studies reveal a molecular network controlled by STK that regulates cell wall properties of the seed coat, demonstrating that developmental regulators controlling organ identity also coordinate specific aspects of cell wall characteristics. PMID:27624758

Effects of molecular geometry on the properties of compressed diamondoid crystals

DOE PAGES

Yang, Fan; Lin, Yu; Baldini, Maria; ...

2016-11-01

Diamondoids are an intriguing group of carbon-based nanomaterials, which combine desired properties of inorganic nanomaterials and small hydrocarbon molecules with atomic-level uniformity. In this Letter, we report the first comparative study on the effect of pressure on a series of diamondoid crystals with systematically varying molecular geometries and shapes, including zero-dimensional (0D) adamantane; one-dimensional (1D) diamantane, [121]tetramantane, [123]tetramantane, and [1212]pentamantane; two-dimensional (2D) [12312]hexamantane; and three-dimensional (3D) triamantane and [1(2,3)4]pentamantane. We find the bulk moduli of these diamondoid crystals are strongly dependent on the diamondoids’ molecular geometry with 3D [1(2,3)4]pentamantane being the least compressible and 0D adamantane being the most compressible.more » These diamondoid crystals possess excellent structural rigidity and are able to sustain large volume deformation without structural failure even after repetitive pressure loading cycles. These properties are desirable for constructing cushioning devices. Furthermore, we also demonstrate that lower diamondoids outperform the conventional cushioning materials in both the working pressure range and energy absorption density.« less

Soft hydrogel materials from elastomeric gluten-mimetic proteins

NASA Astrophysics Data System (ADS)

Bagheri, Mehran; Scott, Shane; Wan, Fan; Dick, Scott; Harden, James; Biomolecular Assemblies Team

2014-03-01

Elastomeric proteins are ubiquitous in both animal and plant tissues, where they are responsible for the elastic response and mechanical resilience of tissues. In addition to fundamental interest in the molecular origins of their elastic behaviour, this class of proteins has great potential for use in biomaterial applications. The structural and elastomeric properties of these proteins are thought to be controlled by a subtle balance between hydrophobic interactions and entropic effects, and in many cases their characteristic properties can be recapitulated by multi-block protein polymers formed from repeats of short, characteristic polypeptide motifs. We have developed biomimetic multi-block protein polymers based on variants of several elastomeric gluten consensus sequences. These proteins include constituents designed to maximize their solubility in aqueous solution and minimize the formation of extended secondary structure. Thus, they are examples of elastic intrinsically disordered proteins. In addition, the proteins have distributed tyrosine residues which allow for inter-molecular crosslinking to form hydrogel networks. In this talk, we present experimental and simulation studies of the molecular and materials properties of these proteins and their assemblies.

Is electronegativity a useful descriptor for the pseudo-alkali metal NH4?

PubMed

Whiteside, Alexander; Xantheas, Sotiris S; Gutowski, Maciej

2011-11-18

Molecular ions in the form of "pseudo-atoms" are common structural motifs in chemistry, with properties that are transferrable between different compounds. We have determined one such property--the electronegativity--for the "pseudo-alkali metal" ammonium (NH(4)), and evaluated its reliability as a descriptor versus the electronegativities of the alkali metals. The computed properties of ammonium's binary complexes with astatine and of selected borohydrides confirm the similarity of NH(4) to the alkali metal atoms, although the electronegativity of NH(4) is relatively large in comparison to its cationic radius. We have paid particular attention to the molecular properties of ammonium (angular anisotropy, geometric relaxation and reactivity), which can cause deviations from the behaviour expected of a conceptual "true alkali metal" with this electronegativity. These deviations allow for the discrimination of effects associated with the molecular nature of NH(4). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation and properties of comb-like surfactants containing poly(ethylene oxide) methyl ether grafts.

PubMed

Zhang, Wei; Du, Zhiping; Chang, Chien-Hsiang; Wang, Guoyong

2009-09-15

The comb-like surfactants, poly(styrene-co-maleic anhydride)-g-(poly(ethylene glycol) monomethyl ether), poly(St-co-MA)-g-(MPEG), have been prepared using a macromonomer approach to get controlled molecular structures. The macromonomer (MAMPEG) was obtained by esterification of poly(ethylene glycol) monomethyl ether with maleic anhydride. Poly(St-co-MA)-g-(MPEG) with various molar ratios of St to MAMPEG (R) were then constructed by radical copolymerization. The comb-like structures of the surfactants were confirmed by infrared and (1)H nuclear magnetic resonance spectroscopy. It is found from gel permeation chromatography characterization that the molecular weight of the surfactants increases as R increases. The polydispersity index was in the range between 1.4 and 2.0 in all the cases. The surfactants with a higher St percentage are less soluble in water due to aggregation. The value of critical aggregation concentration (CAC) and the surface tension at the CAC (gamma(CAC)) decrease as R increases. The steady-shear measurements show that the surfactant solutions at 50 g/L are dilatant fluids. In addition, it appears that there are two break points in the viscosity-shear rate curve. Both break points increase with increasing R. It can therefore be concluded that the properties of comb-like surfactants poly(St-co-MA)-g-(MPEG) are related to molecular structure. The results demonstrate that the properties of these comb-like surfactants can be tailored through appropriate molecular design.

Structural properties and glass transition in Aln clusters

NASA Astrophysics Data System (ADS)

Sun, D. Y.; Gong, X. G.

1998-02-01

We have studied the structural and dynamical properties of several Aln clusters by the molecular-dynamics method combined with simulated annealing. The well-fitted glue potential is used to describe the interatomic interaction. The obtained atomic structures for n=13, 55, and 147 are in agreement with results from ab initio calculations. Our results have demonstrated that the disordered cluster Al43 can be considered as a glass cluster. The obtained thermal properties of glass cluster Al43 are clearly different from the results for high-symmetry clusters, its melting behavior has properties similar to those of a glass solid. The present studies also show that the surface melting behavior does not exist in the studied Aln clusters.

A realistic molecular model of cement hydrates.

PubMed

Pellenq, Roland J-M; Kushima, Akihiro; Shahsavari, Rouzbeh; Van Vliet, Krystyn J; Buehler, Markus J; Yip, Sidney; Ulm, Franz-Josef

2009-09-22

Despite decades of studies of calcium-silicate-hydrate (C-S-H), the structurally complex binder phase of concrete, the interplay between chemical composition and density remains essentially unexplored. Together these characteristics of C-S-H define and modulate the physical and mechanical properties of this "liquid stone" gel phase. With the recent determination of the calcium/silicon (C/S = 1.7) ratio and the density of the C-S-H particle (2.6 g/cm(3)) by neutron scattering measurements, there is new urgency to the challenge of explaining these essential properties. Here we propose a molecular model of C-S-H based on a bottom-up atomistic simulation approach that considers only the chemical specificity of the system as the overriding constraint. By allowing for short silica chains distributed as monomers, dimers, and pentamers, this C-S-H archetype of a molecular description of interacting CaO, SiO2, and H2O units provides not only realistic values of the C/S ratio and the density computed by grand canonical Monte Carlo simulation of water adsorption at 300 K. The model, with a chemical composition of (CaO)(1.65)(SiO2)(H2O)(1.75), also predicts other essential structural features and fundamental physical properties amenable to experimental validation, which suggest that the C-S-H gel structure includes both glass-like short-range order and crystalline features of the mineral tobermorite. Additionally, we probe the mechanical stiffness, strength, and hydrolytic shear response of our molecular model, as compared to experimentally measured properties of C-S-H. The latter results illustrate the prospect of treating cement on equal footing with metals and ceramics in the current application of mechanism-based models and multiscale simulations to study inelastic deformation and cracking.

Importance of Kier-Hall topological indices in the QSAR of anticancer drug design.

PubMed

Nandi, Sisir; Bagchi, Manish C

2012-06-01

An important area of theoretical drug design research is quantitative structure activity relationship (QSAR) using structural invariants. The impetus for this research trend comes from various directions. Researchers in chemical documentation have searched for a set of invariants which will be more convenient than the adjacency matrix (or connection table) for the storage and comparison of chemical structures. Molecular structure can be looked upon as the representation of the relationship among its various constituents. The term molecular structure represents a set of nonequivalent and probably disjoint concepts. There is no reason to believe that when we discuss diverse topics (e.g. chemical synthesis, reaction rates, spectroscopic transitions, reaction mechanisms, and ab initio calculations) using the notion of molecular structure, the different meanings we attach to the single term molecular structure originate from the same fundamental concept. On the contrary, there is a theoretical and philosophical basis for the non-homogeneity of concepts covered by the term molecular structure. In the context of molecular science, the various concepts of molecular structure (e.g. classical valence bond representations, various chemical graph-theoretic representations, ball and spoke model of a molecule, representation of a molecule by minimum energy conformation, semi symbolic contour map of a molecule, or symbolic representation of chemical species by Hamiltonian operators) are model objects derived through different abstractions of the same chemical reality. In each instance, the equivalence class (concept or model of molecular structure) is generated by selecting certain aspects while ignoring some unique properties of those actual events. This explains the plurality of the concept of molecular structure and their autonomous nature, the word autonomous being used in the same sense that one concept is not logically derived from the other. At the most fundamental level, the structural model of an assembled entity (e.g. a molecule consisting of atoms) may be defined as the pattern of relationship among its parts as distinct from the values associated with them. Constitutional formulae of molecules are graphs where vertices represent the set of atoms and edges represent chemical bonds. The pattern of connectedness of atoms in a molecule is preserved by constitutional graphs. A graph (more correctly a non-directed graph) G = [V, E] consists of a finite non-empty set V of points together with a prescribed set E of unordered pairs of distinct points of V. Thus the mathematical characterization of structures represents structural invariants having successful applications in chemical documentation, characterization of molecular branching, enumeration of molecular constitutional associated with a particular empirical formula, calculation of quantum chemical parameters for the generation of quantitative structure-property-activity correlations. Kier developed a number of structural invariants which are now-a-days called as topological indices with wide range of practical applications for QSAR and drug design. The present paper is restricted to the review of Kier-Hall topological indices for QSAR and anticancer drug design for 2,5-bis(1-aziridinyl) 1,4-benzoquinone (BABQ), pyridopyrimidine, 4-anilinoquinazoline and 2-Phenylindoles compounds utilizing various statistical multivariate regression analyses.

Abnormal characteristics of binary molecular clusters in DMSO–ethanol mixtures under external electric fields

NASA Astrophysics Data System (ADS)

Wu, Zhiyan; Huang, Kama

2018-05-01

For the nonlinearly phenomena on the dielectric properties of dimethyl sulfoxide (DMSO)-ethanol mixtures under a low intensity microwave field, we propose a conjecture that there exist some abnormal molecular clusters. To interpret the mechanism of abnormal phenomena and confirm our conjecture about the existence of abnormal molecular clusters, an in-depth investigation about the structure evolutions of (DMSO)m(C2H5OH)n (m = 0-4; n = 0-4; m + n ≤ 4) molecular clusters induced by external electric fields has been given by using density functional theory. The results show that there exist some binary molecular clusters with large cluster radii in mixtures, and some of them are unstable under exposure of electric fields. It implies that the existence of certain abnormal molecular clusters in DMSO-ethanol mixtures results in their abnormality of dielectric properties.

Protonated o-semiquinone radical as a mimetic of the humic acids native radicals: A DFT approach to the molecular structure and EPR properties

NASA Astrophysics Data System (ADS)

Witwicki, Maciej; Jezierska, Julia

2012-06-01

Organic radicals are known to be an indispensable component of the humic acids (HA) structure. In HA two forms of radicals, stable (native) and short-lived (transient), are identified. Importantly, these radical forms can be easily differentiated by electron paramagnetic resonance (EPR) spectroscopy. This article provides a DFT-based insight into the electronic and molecular structure of the native radicals. The molecular models including an increase of the radical aromaticity and the hydrogen bonding between the radical and other functional groups of HA are taken under investigation. In consequence the interesting pieces of information on the structure of the native radical centers in HA are revealed and discussed, especially in terms of differences between the electronic structure of the native and transient forms.

A Cobalt Supramolecular Triple-Stranded Helicate-based Discrete Molecular Cage

PubMed Central

Mai, Hien Duy; Kang, Philjae; Kim, Jin Kyung; Yoo, Hyojong

2017-01-01

We report a strategy to achieve a discrete cage molecule featuring a high level of structural hierarchy through a multiple-assembly process. A cobalt (Co) supramolecular triple-stranded helicate (Co-TSH)-based discrete molecular cage (1) is successfully synthesized and fully characterized. The solid-state structure of 1 shows that it is composed of six triple-stranded helicates interconnected by four linking cobalt species. This is an unusual example of a highly symmetric cage architecture resulting from the coordination-driven assembly of metallosupramolecular modules. The molecular cage 1 shows much higher CO2 uptake properties and selectivity compared with the separate supramolecular modules (Co-TSH, complex 2) and other molecular platforms. PMID:28262690

Structure and dynamics of mica-confined films of [C10C1Pyrr][NTf2] ionic liquid

NASA Astrophysics Data System (ADS)

Freitas, Adilson Alves de; Shimizu, Karina; Smith, Alexander M.; Perkin, Susan; Canongia Lopes, José Nuno

2018-05-01

The structure of the ionic liquid 1-decyl-1-methylpyrrolidinium bis[(trifluoromethane)sulfonyl]imide, [C10C1Pyrr][NTf2], has been probed using Molecular Dynamics (MD) simulations. The simulations endeavour to model the behaviour of the ionic liquid in bulk isotropic conditions and also at interfaces and in confinement. The MD results have been confronted and validated with scattering and surface force experiments reported in the literature. The calculated structure factors, distribution functions, and density profiles were able to provide molecular and mechanistic insights into the properties of these long chain ionic liquids under different conditions, in particular those that lead to the formation of multi-layered ionic liquid films in confinement. Other properties inaccessible to experiment such as in-plane structures and relaxation rates within the films have also been analysed. Overall the work contributes structural and dynamic information relevant to many applications of ionic liquids with long alkyl chains, ranging from nanoparticle synthesis to lubrication.

Conjugation in multi-tetrazole derivatives: a new design direction for energetic materials.

PubMed

Sun, Shuyang; Lu, Ming

2018-06-23

Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these molecules with conjugated structures showed low energies of their crystal structures, molecular layering in their crystals, high average ESPs, high multicenter bond order values, and enhanced detonation properties. The derivative 1,2-di(1H-tetrazol-5-yl)diazene (N2) was predicted to have the best density (1.87 g/cm 3 ), detonation velocity (9006 m/s), and detonation pressure (36.8 GPa) of the designed molecules, while its total crystal energy was low, suggesting that it is relatively stable. Its sensitivity was also low, as the molecular stacking that occurs in its crystal allows external forces to be dissipated into movements of crystal layers. Finally, its multicenter bond order was high, indicating a highly conjugated structure.

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

PubMed

Zhang, Z; Fenter, P; Cheng, L; Sturchio, N C; Bedzyk, M J; Predota, M; Bandura, A; Kubicki, J D; Lvov, S N; Cummings, P T; Chialvo, A A; Ridley, M K; Bénézeth, P; Anovitz, L; Palmer, D A; Machesky, M L; Wesolowski, D J

2004-06-08

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Effects of growth rate on structural property and adatom migration behaviors for growth of GaInNAs/GaAs (001) by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Jingling; Gao, Peng; Zhang, Shuguang; Wen, Lei; Gao, Fangliang; Li, Guoqiang

2018-03-01

We have investigated the structural properties and the growth mode of GaInNAs films prepared at different growth rates (Rg) by molecular beam epitaxy. The crystalline structure is studied by high resolution X-ray diffraction, and the evolution of GaInNAs film surface morphologies is studied by atomic force microscopy. It is found that both the crystallinity and the surface roughness are improved by increasing Rg, and the change in the growth mode is attributed to the adatom migration behaviors particularly for In atoms, which is verified by elemental analysis. In addition, we have presented some theoretical calculation results related to the N adsorption energy to show the unique N migration behavior, which is instructive to interpret the growth mechanism of GaInNAs films.

Viscoelastic properties of model segments of collagen molecules.

PubMed

Gautieri, Alfonso; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

2012-03-01

Collagen is the prime construction material in vertebrate biology, determining the mechanical behavior of connective tissues such as tendon, bone and skin. Despite extensive efforts in the investigation of the origin of collagen unique mechanical properties, a deep understanding of the relationship between molecular structure and mechanical properties remains elusive, hindered by the complex hierarchical structure of collagen-based tissues. In particular, although extensive studies of viscoelastic properties have been pursued at the macroscopic (fiber/tissue) level, fewer investigations have been performed at the smaller scales, including in particular collagen molecules and fibrils. These scales are, however, important for a complete understanding of the role of collagen as an important constituent in the extracellular matrix. Here, using an atomistic modeling approach, we perform in silico creep tests of a collagen-like peptide, monitoring the strain-time response for different values of applied external load. The results show that individual collagen molecules exhibit a nonlinear viscoelastic behavior, with a Young's modulus increasing from 6 to 16GPa (for strains up to 20%), a viscosity of 3.84.±0.38Pa·s, and a relaxation time in the range of 0.24-0.64ns. The single molecule viscosity, for the first time reported here, is several orders of magnitude lower than the viscosity found for larger-scale single collagen fibrils, suggesting that the viscous behavior of collagen fibrils and fibers involves additional mechanisms, such as molecular sliding between collagen molecules within the fibril or the effect of relaxation of larger volumes of solvent. Based on our molecular modeling results we propose a simple structural model that describes collagen tissue as a hierarchical structure, providing a bottom-up description of elastic and viscous properties form the properties of the tissue basic building blocks. Copyright © 2011 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

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

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

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

Multidisciplinary research in space sciences and engineering with emphasis on theoretical chemistry

NASA Technical Reports Server (NTRS)

Hirschfelder, J. O.; Curtiss, C. F.

1974-01-01

A broad program is reported of research in theoretical chemistry, particularly in molecular quantum and statistical mechanics, directed toward determination of the physical and chemical properties of materials, relation of these macroscopic properties to properties of individual molecules, and determination of the structure and properties of the individual molecules. Abstracts are presented for each research project conducted during the course of the program.

Random Walks on a Simple Cubic Lattice, the Multinomial Theorem, and Configurational Properties of Polymers

ERIC Educational Resources Information Center

Hladky, Paul W.

2007-01-01

Random-climb models enable undergraduate chemistry students to visualize polymer molecules, quantify their configurational properties, and relate molecular structure to a variety of physical properties. The model could serve as an introduction to more elaborate models of polymer molecules and could help in learning topics such as lattice models of…

Anticancer and cancer preventive properties of marine polysaccharides: some results and prospects.

PubMed

Fedorov, Sergey N; Ermakova, Svetlana P; Zvyagintseva, Tatyana N; Stonik, Valentin A

2013-12-02

Many marine-derived polysaccharides and their analogues have been reported as showing anticancer and cancer preventive properties. These compounds demonstrate interesting activities and special modes of action, differing from each other in both structure and toxicity profile. Herein, literature data concerning anticancer and cancer preventive marine polysaccharides are reviewed. The structural diversity, the biological activities, and the molecular mechanisms of their action are discussed.

Molecular Dynamics Simulation Of Novel Elastomer Nanocomposites: Structure Design And Property Prediction

NASA Astrophysics Data System (ADS)

Liu, Jun; Zhang, Liqun

In this talk, by employing molecular dynamics simulation, we aim to provide the structure design and property prediction of novel elastomer nanocomposites(ENCs), by considering three typical systems such as physical compounding, self-assembly and end-linked systems. We examine the dispersion, interfacial interaction and the resulting static and dynamic mechanical properties of each system. Emphasis is placed on how to tune the visco-elasticity and decrease the dynamic hysteresis loss of ENCs, by considering to introduce the flexible nanoparticles(NPs) with reversible mechanical deformation such as carbon nanosprings and graphene nanoribbon, or by achieving a homogeneous distribution of NPs in the elastomeric polymer matrix together with decreasing the mobility of the end-groups of polymer chains. In particular, the end-linked system exhibits both excellent static and dynamic mechanical properties, independent of the temperature. This novel ENCs could provide some useful guidances for the fabrication of high performance ENCs tailored for tire tread of green tires by cutting the fuel consumption.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Striped gold nanoparticles: New insights from molecular dynamics simulations

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

Velachi, Vasumathi, E-mail: vasuphy@gmail.com; Cordeiro, M. Natália D. S., E-mail: ncordeir@fc.up.pt; Bhandary, Debdip

Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199–3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols’ arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper,more » we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl’s chain length, the length difference between the thiol mixtures, and solvent properties.« less

Milling of rice grains: effects of starch/flour structures on gelatinization and pasting properties.

PubMed

Hasjim, Jovin; Li, Enpeng; Dhital, Sushil

2013-01-30

Starch gelatinization and flour pasting properties were determined and correlated with four different levels of starch structures in rice flour, i.e. flour particle size, degree of damaged starch granules, whole molecular size, and molecular branching structure. Onset starch-gelatinization temperatures were not significantly different among all flour samples, but peak and conclusion starch-gelatinization temperatures were significantly different and were strongly correlated with the flour particle size, indicating that rice flour with larger particle size has a greater barrier for heat transfer. There were slight differences in the enthalpy of starch gelatinization, which are likely associated with the disruption of crystalline structure in starch granules by the milling processes. Flours with volume-median diameter ≥56 μm did not show a defined peak viscosity in the RVA viscogram, possibly due to the presence of native protein and/or cell-wall structure stabilizing the swollen starch granules against the rupture caused by shear during heating. Furthermore, RVA final viscosity of flour was strongly correlated with the degree of damage to starch granules, suggesting the contribution of granular structure, possibly in swollen form. The results from this study allow the improvement in the manufacture and the selection criteria of rice flour with desirable gelatinization and pasting properties. Copyright © 2012 Elsevier Ltd. All rights reserved.

Functionalization-induced changes in the structural and physical properties of amorphous polyaniline: a first-principles and molecular dynamics study.

PubMed

Chen, X P; Liang, Q H; Jiang, J K; Wong, Cell K Y; Leung, Stanley Y Y; Ye, H Y; Yang, D G; Ren, T L

2016-02-09

In this paper, we present a first-principles and molecular dynamics study to delineate the functionalization-induced changes in the local structure and the physical properties of amorphous polyaniline. The results of radial distribution function (RDF) demonstrate that introducing -SO3(-)Na(+) groups at phenyl rings leads to the structural changes in both the intrachain and interchain ordering of polyaniline at shorter distances (≤5 Å). An unique RDF feature in 1.8-2.1 Å regions is usually observed in both the interchain and intrachain RDF profiles of the -SO3(-)Na(+) substituted polymer (i.e. Na-SPANI). Comparative studies of the atom-atom pairs, bond structures, torsion angles and three-dimensional structures show that EB-PANI has much better intrachain ordering than that of Na-SPANI. In addition, investigation of the band gap, density of states (DOS), and absorption spectra indicates that the derivatization at ring do not substantially alter the inherent electronic properties but greatly change the optical properties of polyaniline. Furthermore, the computed diffusion coefficient of water in Na-SPANI is smaller than that of EB-PANI. On the other hand, the Na-SPANI shows a larger density than that of EB-PANI. The computed RDF profiles, band gaps, absorption spectra, and diffusion coefficients are in quantitative agreement with the experimental data.

The Relationship Between Chemical Structure and Dielectric Properties of Plasma-Enhanced Chemical Vapor Deposited Polymer Thin Films (Postprint)

DTIC Science & Technology

2007-01-01

C6H6, Aldrich Co., liquid , high performance liquid chromatography (HPLC) grade with a purity of 99.9%) and octafluorocyclobutane (C4F8, OFCB...attributed to the lack of molecular mobility (confined by the crosslinking) and low ionic polarization of the molecular structures [6]. The frequency...in dielectric constant at low frequencies can be traced to orientational polarizations of trapped free radicals, unpaired electron sites, oligomeric

Molecular chaperones: functional mechanisms and nanotechnological applications

NASA Astrophysics Data System (ADS)

Rosario Fernández-Fernández, M.; Sot, Begoña; María Valpuesta, José

2016-08-01

Molecular chaperones are a group of proteins that assist in protein homeostasis. They not only prevent protein misfolding and aggregation, but also target misfolded proteins for degradation. Despite differences in structure, all types of chaperones share a common general feature, a surface that recognizes and interacts with the misfolded protein. This and other, more specialized properties can be adapted for various nanotechnological purposes, by modification of the original biomolecules or by de novo design based on artificial structures.

The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.

Synthesis, characterization, crystal structure and quantum chemical investigations of three novel coumarin-benzenesulfonohydrazide derivatives

NASA Astrophysics Data System (ADS)

Chethan Prathap, K. N.; Lokanath, N. K.

2018-04-01

Coumarin derivatives are an important class of heterocyclic compounds due to their physical and biological properties. Coumarin derivatives have been identified with many significant electro-optical properties and biological activities. Three novel coumarin derivatives containing benzene sulfonohydrazide group were synthesized by condensation reaction. The synthesized compounds were characterized by various spectroscopic techniques (Mass, 1H/13C NMR and FTIR). Thermal and optical properties were investigated by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and UV-Vis spectroscopic studies. Finally their structures were confirmed by single crystal X-ray diffraction (XRD) studies. The three compounds exhibit diverse intermolecular interactions, as observed by the crystal packing and Hirshfeld surface analysis. Further, their structures were optimized by density functional theory (DFT) calculations using B3LYP hybrid functionals with 6-311G+(d,p) level basis set. The Mulliken charge, molecular electrostatic potential (MEP), frontier molecular orbitals (HOMO-LUMO) were investigated. The experimentally determined parameters were compared with those calculated theoretically and they complement each other with a very good correlation. The transitions among the molecular orbitals were investigated using time-dependent density functional theory (TD-DFT) and the electronic absorption spectra obtained showed very good agreement with the experimentally measured UV-Vis spectra. Furthermore, non-linear optical (NLO) properties were investigated by calculating polarizabilities and hyperpolarizabilities. All three compounds exhibit significantly high hyperpolarizabilities compared to the reference material urea, which makes them potential candidates for NLO applications.

Understanding polymorphism in organic semiconductor thin films through nanoconfinement.

PubMed

Diao, Ying; Lenn, Kristina M; Lee, Wen-Ya; Blood-Forsythe, Martin A; Xu, Jie; Mao, Yisha; Kim, Yeongin; Reinspach, Julia A; Park, Steve; Aspuru-Guzik, Alán; Xue, Gi; Clancy, Paulette; Bao, Zhenan; Mannsfeld, Stefan C B

2014-12-10

Understanding crystal polymorphism is a long-standing challenge relevant to many fields, such as pharmaceuticals, organic semiconductors, pigments, food, and explosives. Controlling polymorphism of organic semiconductors (OSCs) in thin films is particularly important given that such films form the active layer in most organic electronics devices and that dramatic changes in the electronic properties can be induced even by small changes in the molecular packing. However, there are very few polymorphic OSCs for which the structure-property relationships have been elucidated so far. The major challenges lie in the transient nature of metastable forms and the preparation of phase-pure, highly crystalline thin films for resolving the crystal structures and evaluating the charge transport properties. Here we demonstrate that the nanoconfinement effect combined with the flow-enhanced crystal engineering technique is a powerful and likely material-agnostic method to identify existing polymorphs in OSC materials and to prepare the individual pure forms in thin films at ambient conditions. With this method we prepared high quality crystal polymorphs and resolved crystal structures of 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene), including a new polymorph discovered via in situ grazing incidence X-ray diffraction and confirmed by molecular mechanic simulations. We further correlated molecular packing with charge transport properties using quantum chemical calculations and charge carrier mobility measurements. In addition, we applied our methodology to a [1]benzothieno[3,2-b][1]1benzothiophene (BTBT) derivative and successfully stabilized its metastable form.

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.

PubMed

Venko, Katja; Roy Choudhury, A; Novič, Marjana

2017-01-01

The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix-helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.

Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

PubMed

Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

2016-08-17

Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

Effects of the amino acid sequence on thermal conduction through β-sheet crystals of natural silk protein.

PubMed

Zhang, Lin; Bai, Zhitong; Ban, Heng; Liu, Ling

2015-11-21

Recent experiments have discovered very different thermal conductivities between the spider silk and the silkworm silk. Decoding the molecular mechanisms underpinning the distinct thermal properties may guide the rational design of synthetic silk materials and other biomaterials for multifunctionality and tunable properties. However, such an understanding is lacking, mainly due to the complex structure and phonon physics associated with the silk materials. Here, using non-equilibrium molecular dynamics, we demonstrate that the amino acid sequence plays a key role in the thermal conduction process through β-sheets, essential building blocks of natural silks and a variety of other biomaterials. Three representative β-sheet types, i.e. poly-A, poly-(GA), and poly-G, are shown to have distinct structural features and phonon dynamics leading to different thermal conductivities. A fundamental understanding of the sequence effects may stimulate the design and engineering of polymers and biopolymers for desired thermal properties.

Structural, dynamic and photophysical properties of a fluorescent dye incorporated in an amorphous hydrophobic polymer bundle.

PubMed

De Mitri, N; Prampolini, G; Monti, S; Barone, V

2014-08-21

The properties of a low molecular weight organic dye, namely 4-naphthyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine, covalently bound to an apolar polyolefin were investigated by means of a multi-level approach, combining classical molecular dynamics simulations, based on purposely parameterized force fields, and quantum mechanical calculations based on density functional theory (DFT) and its time-dependent extension (TD-DFT). The structure and dynamics of the dye in its embedding medium were analyzed and discussed taking the entangling effect of the surrounding polymer into account, and also by comparing the results to those obtained for a different environment, i.e. toluene solution. Finally, the influence was investigated of long lived cages found in the polymeric embedding on photophysical properties, in terms of the slow and fast dye's internal dynamics, by comparing computed IR and UV spectra with their experimental counterparts.

Microscopic properties of ionic liquid/organic semiconductor interfaces revealed by molecular dynamics simulations.

PubMed

Yokota, Yasuyuki; Miyamoto, Hiroo; Imanishi, Akihito; Takeya, Jun; Inagaki, Kouji; Morikawa, Yoshitada; Fukui, Ken-Ichi

2018-05-09

Electric double-layer transistors based on ionic liquid/organic semiconductor interfaces have been extensively studied during the past decade because of their high carrier densities at low operation voltages. Microscopic structures and the dynamics of ionic liquids likely determine the device performance; however, knowledge of these is limited by a lack of appropriate experimental tools. In this study, we investigated ionic liquid/organic semiconductor interfaces using molecular dynamics to reveal the microscopic properties of ionic liquids. The organic semiconductors include pentacene, rubrene, fullerene, and 7,7,8,8-tetracyanoquinodimethane (TCNQ). While ionic liquids close to the substrate always form the specific layered structures, the surface properties of organic semiconductors drastically alter the ionic dynamics. Ionic liquids at the fullerene interface behave as a two-dimensional ionic crystal because of the energy gain derived from the favorable electrostatic interaction on the corrugated periodic substrate.

Application of atomic force microscopy as a nanotechnology tool in food science.

PubMed

Yang, Hongshun; Wang, Yifen; Lai, Shaojuan; An, Hongjie; Li, Yunfei; Chen, Fusheng

2007-05-01

Atomic force microscopy (AFM) provides a method for detecting nanoscale structural information. First, this review explains the fundamentals of AFM, including principle, manipulation, and analysis. Applications of AFM are then reported in food science and technology research, including qualitative macromolecule and polymer imaging, complicated or quantitative structure analysis, molecular interaction, molecular manipulation, surface topography, and nanofood characterization. The results suggested that AFM could bring insightful knowledge on food properties, and the AFM analysis could be used to illustrate some mechanisms of property changes during processing and storage. However, the current difficulty in applying AFM to food research is lacking appropriate methodology for different food systems. Better understanding of AFM technology and developing corresponding methodology for complicated food systems would lead to a more in-depth understanding of food properties at macromolecular levels and enlarge their applications. The AFM results could greatly improve the food processing and storage technologies.

Multiscale Modeling of PEEK Using Reactive Molecular Dynamics Modeling and Micromechanics

NASA Technical Reports Server (NTRS)

Pisani, William A.; Radue, Matthew; Chinkanjanarot, Sorayot; Bednarcyk, Brett A.; Pineda, Evan J.; King, Julia A.; Odegard, Gregory M.

2018-01-01

Polyether ether ketone (PEEK) is a high-performance, semi-crystalline thermoplastic that is used in a wide range of engineering applications, including some structural components of aircraft. The design of new PEEK-based materials requires a precise understanding of the multiscale structure and behavior of semi-crystalline PEEK. Molecular Dynamics (MD) modeling can efficiently predict bulk-level properties of single phase polymers, and micromechanics can be used to homogenize those phases based on the overall polymer microstructure. In this study, MD modeling was used to predict the mechanical properties of the amorphous and crystalline phases of PEEK. The hierarchical microstructure of PEEK, which combines the aforementioned phases, was modeled using a multiscale modeling approach facilitated by NASA's MSGMC. The bulk mechanical properties of semi-crystalline PEEK predicted using MD modeling and MSGMC agree well with vendor data, thus validating the multiscale modeling approach.

Poly(trifluoromethyl)azulenes: structures and acceptor properties

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

Clikeman, Tyler T.; Bukovsky, Eric V.; Kuvychko, Igor V.

2014-07-10

Azulene is a non-alternant, non-benzenoid aromatic hydrocarbon with an intense blue colour, a dipole moment of 1.0 D,1 positive electron affinity, and an “anomalous” emission from the second excited state in violation of Kasha’s rule.2,3 Azulene’s unique properties have potential uses in molecular switches,4,5 molecular diodes,6 organic photovoltaics,7 and charge transfer complexes.8-12 Introduction of electron-withdrawing groups to the azulenic core, such as CN,8,13,14 halogens,15-19 and CF3,20,21 can enhance certain electrical and photophysical properties. In this work, we report six new trifluoromethyl derivatives of azulene (AZUL), three isomers of AZUL(CF3)3 and three isomers of AZUL(CF3)4, and the first X-ray structure ofmore » a π-stacked donor-acceptor complex of a trifluoromethyl azulene with donor pyrene.« less

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Ligand structure and mechanical properties of single-nanoparticle-thick membranes.

PubMed

Salerno, K Michael; Bolintineanu, Dan S; Lane, J Matthew D; Grest, Gary S

2015-06-01

The high mechanical stiffness of single-nanoparticle-thick membranes is believed to result from the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with a nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH(3)) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Moreover, the particular end group (COOH or CH(3)) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer

NASA Astrophysics Data System (ADS)

Schmidt, Matthew; Roy, Pierre-Nicholas

2018-03-01

We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Molecular structure, vibrational spectra, NLO and MEP analysis of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II)

NASA Astrophysics Data System (ADS)

Tanak, Hasan; Toy, Mehmet

2013-11-01

The molecular geometry and vibrational frequencies of bis[2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN]zinc(II) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional method (B3LYP) with 6-311G(d,p) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The energetic and atomic charge behavior of the title compound in solvent media has been examined by applying the Onsager and the polarizable continuum model. To investigate second order nonlinear optical properties of the title compound, the electric dipole (μ), linear polarizability (α) and first-order hyperpolarizability (β) were computed using the density functional B3LYP and CAM-B3LYP methods with the 6-31+G(d) basis set. According to our calculations, the title compound exhibits nonzero (β) value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), frontier molecular orbitals, and thermodynamic properties were performed at B3LYP/6-311G(d,p) level of theory.

Synthesis, XRD crystal structure, spectroscopic characterization, local reactive properties using DFT and molecular dynamics simulations and molecular docking study of (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

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

2017-06-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. 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 to fit the title compound into the binding site of MOA-B enzyme.

Structures, mechanical properties, equations of state, and electronic properties of β-HMX under hydrostatic pressures: a DFT-D2 study.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; De, Suvranu

2014-10-07

We report the hydrostatic compression studies of the β-polymorph of a cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using DFT-D2, a first-principles calculation based on density functional theory (DFT) with van der Waals (vdW) corrections. The molecular structure, mechanical properties, electronic properties, and equations of state of β-HMX are investigated. For the first time, we predict the elastic constants of β-HMX using DFT-D2 studies. The equations of state under hydrostatic compression are studied for pressures up to 100 GPa. We found that the N-N bonds along the minor axis are responsible for the sensitivity of β-HMX. The analysis of the charge distribution shows that the electronic charge is transferred from hydrogen atoms to nitro groups with the amount of 0.131 and 0.064e for the nitro groups along the minor axis and major axis, respectively, when pressure changes from 0 GPa to 100 GPa. The electronic energy band gap changes from direct at a pressure of 0 GPa to indirect at a pressure of 50 GPa and higher. The band gap decreases with respect to an increase in pressure, implying that the impact sensitivity increases with compression. Our study suggests that the van der Waals interactions are critically important in modeling the mechanical properties of this molecular crystal.

Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

PubMed

Bressuire-Isoard, Christelle; Broussolle, Véronique; Carlin, Frédéric

2018-05-17

Bacterial spores are resistant to physical and chemical insults, which make them a major concern for public health and for industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection, and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination, and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.

Relationships between chemical structure, mechanical properties and materials processing in nanopatterned organosilicate fins.

PubMed

Stan, Gheorghe; Gates, Richard S; Hu, Qichi; Kjoller, Kevin; Prater, Craig; Jit Singh, Kanwal; Mays, Ebony; King, Sean W

2017-01-01

The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR) and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM) to investigate the fabrication of 20-500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10-20 nm. While the observed structure-property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential.

Toward Measuring Galactic Dense Molecular Gas Properties and 3D Distribution with Hi-GAL

NASA Astrophysics Data System (ADS)

Zetterlund, Erika; Glenn, Jason; Maloney, Phil

2016-01-01

The Herschel Space Observatory's submillimeter dust continuum survey Hi-GAL provides a powerful new dataset for characterizing the structure of the dense interstellar medium of the Milky Way. Hi-GAL observed a 2° wide strip covering the entire 360° of the Galactic plane in broad bands centered at 70, 160, 250, 350, and 500 μm, with angular resolution ranging from 10 to 40 arcseconds. We are adapting a molecular cloud clump-finding algorithm and a distance probability density function distance-determination method developed for the Bolocam Galactic Plane Survey (BGPS) to the Hi-GAL data. Using these methods we expect to generate a database of 105 cloud clumps, derive distance information for roughly half the clumps, and derive precise distances for approximately 20% of them. With five-color photometry and distances, we will measure the cloud clump properties, such as luminosities, physical sizes, and masses, and construct a three-dimensional map of the Milky Way's dense molecular gas distribution.The cloud clump properties and the dense gas distribution will provide critical ground truths for comparison to theoretical models of molecular cloud structure formation and galaxy evolution models that seek to emulate spiral galaxies. For example, such models cannot resolve star formation and use prescriptive recipes, such as converting a fixed fraction of interstellar gas to stars at a specified interstellar medium density threshold. The models should be compared to observed dense molecular gas properties and galactic distributions.As a pilot survey to refine the clump-finding and distance measurement algorithms developed for BGPS, we have identified molecular cloud clumps in six 2° × 2° patches of the Galactic plane, including one in the inner Galaxy along the line of sight through the Molecular Ring and the termination of the Galactic bar and one toward the outer Galaxy. Distances have been derived for the inner Galaxy clumps and compared to Bolocam Galactic Plane Survey results. We present the pilot survey clump catalog, distances, clump properties, and a comparison to BGPS.

Bismuth-, Tin-, and Lead-Containing Metal-Organic Materials: Synthesis, Structure, Photoluminescence, Second Harmonic Generation, and Ferroelectric Properties

NASA Astrophysics Data System (ADS)

Wibowo, Arief Cahyo

Metal-Organic Materials (MOMs) contain metal moieties and organic ligands that combine to form discrete (e.g. metal-organic polyhedra, spheres or nanoballs, metal-organic polygons) or polymeric structures with one-, two-, or three-dimensional periodicities that can exhibit a variety of properties resulting from the presence of the metal moieties and/or ligand connectors in the structure. To date, MOMs with a range of functional attributes have been prepared, including record-breaking porosity, catalytic properties, molecular magnetism, chemical separations and sensing ability, luminescence and NLO properties, multiferroic, ferroelectric, and switchable molecular dielectric properties. We are interested in synthesizing non-centrosymmetric MOM single crystals possessing one of the ten polar space groups required for non-linear optical properties (such as second harmonic generation) and ferroelectric applications. This thesis is divided into two main parts: materials with optical properties, such as photoluminescence and materials for targeted applications such as second harmonic generation and ferroelectric properties. This thesis starts with an introduction describing material having centrosymmetric, non-polar space groups, single crystals structures and their photoluminescence properties. These crystals exhibit very interesting and rare structures as well as interesting photoluminescence properties. Chapters 2-5 of this thesis focus on photoluminescent properties of new MOMs, and detail the exploratory research involving the comparatively rare bismuth, lead, and tin coordination polymers. Specifically, the formation of single white-light emitting phosphors based on the combination of bismuth or lead with pyridine-2,5-dicarboxylate is discussed (Chapter 2). The observation of a new Bi2O2 layer and a new Bi4O 3 chain in bismuth terephthalate-based coordination polymers is presented in Chapter 3, while the formation of diverse structures of tin-based coordination polymer ranging from 1D supramolecular structures to true 3D coordination polymers is covered in Chapter 4. The observation of a new 2D Kagome lattice and unique layered perovskite-type bismuth-based coordination polymers and their photoluminescence properties is the focus of Chapter 5. In chapters 6 and 7, a successful approach to implement our novel hybrid strategy for synthesizing enantiomerically pure single crystals consisting of Second Order Jahn Teller (SOJT)-possessing main group metal cations, specifically bismuth and tin, and homochiral ligands or unsymmetric ligands is discussed. The new MOMs with polar space groups exhibit second harmonic generation and have potential for ferroelectric properties.

Supercomputer applications in molecular modeling.

PubMed

Gund, T M

1988-01-01

An overview of the functions performed by molecular modeling is given. Molecular modeling techniques benefiting from supercomputing are described, namely, conformation, search, deriving bioactive conformations, pharmacophoric pattern searching, receptor mapping, and electrostatic properties. The use of supercomputers for problems that are computationally intensive, such as protein structure prediction, protein dynamics and reactivity, protein conformations, and energetics of binding is also examined. The current status of supercomputing and supercomputer resources are discussed.

Improving of Mechanical and Shape-Memory Properties in Hyperbranched Epoxy Shape-Memory Polymers

NASA Astrophysics Data System (ADS)

Santiago, David; Fabregat-Sanjuan, Albert; Ferrando, Francesc; De la Flor, Silvia

2016-09-01

A series of shape-memory epoxy polymers were synthesized using an aliphatic amine and two different commercial hyperbranched poly(ethyleneimine)s with different molecular weights as crosslinking agents. Thermal, mechanical, and shape-memory properties in materials modified with different hyperbranched polymers were analyzed and compared in order to establish the effect of the structure and the molecular weight of the hyperbranched polymers used. The presence of hyperbranched polymers led to more heterogeneous networks, and the crosslinking densities of which increase as the hyperbranched polymer content increases. The transition temperatures can be tailored from 56 to 117 °C depending on the molecular weight and content of the hyperbranched polymer. The mechanical properties showed excellent values in all formulations at room temperature and, specially, at T_{{g}}^{{E^' with stress at break as high as 15 MPa and strain at break as high as 60 %. The shape-memory performances revealed recovery ratios around 95 %, fixity ratios around 97 %, and shape-recovery velocities as high as 22 %/min. The results obtained in this study reveal that hyperbranched polymers with different molecular weights can be used to enhance the thermal and mechanical properties of epoxy-based SMPs while keeping excellent shape-memory properties.

Potential human cholesterol esterase inhibitor design: benefits from the molecular dynamics simulations and pharmacophore modeling studies.

PubMed

John, Shalini; Thangapandian, Sundarapandian; Lee, Keun Woo

2012-01-01

Human pancreatic cholesterol esterase (hCEase) is one of the lipases found to involve in the digestion of large and broad spectrum of substrates including triglycerides, phospholipids, cholesteryl esters, etc. The presence of bile salts is found to be very important for the activation of hCEase. Molecular dynamic simulations were performed for the apoform and bile salt complexed form of hCEase using the co-ordinates of two bile salts from bovine CEase. The stability of the systems throughout the simulation time was checked and two representative structures from the highly populated regions were selected using cluster analysis. These two representative structures were used in pharmacophore model generation. The generated pharmacophore models were validated and used in database screening. The screened hits were refined for their drug-like properties based on Lipinski's rule of five and ADMET properties. The drug-like compounds were further refined by molecular docking simulation using GOLD program based on the GOLD fitness score, mode of binding, and molecular interactions with the active site amino acids. Finally, three hits of novel scaffolds were selected as potential leads to be used in novel and potent hCEase inhibitor design. The stability of binding modes and molecular interactions of these final hits were re-assured by molecular dynamics simulations.

Nano-Sized Cyclodextrin-Based Molecularly Imprinted Polymer Adsorbents for Perfluorinated Compounds—A Mini-Review

PubMed Central

Karoyo, Abdalla H.; Wilson, Lee D.

2015-01-01

Recent efforts have been directed towards the design of efficient and contaminant selective remediation technology for the removal of perfluorinated compounds (PFCs) from soils, sediments, and aquatic environments. While there is a general consensus on adsorption-based processes as the most suitable methodology for the removal of PFCs from aquatic environments, challenges exist regarding the optimal materials design of sorbents for selective uptake of PFCs. This article reviews the sorptive uptake of PFCs using cyclodextrin (CD)-based polymer adsorbents with nano- to micron-sized structural attributes. The relationship between synthesis of adsorbent materials and their structure relate to the overall sorption properties. Hence, the adsorptive uptake properties of CD-based molecularly imprinted polymers (CD-MIPs) are reviewed and compared with conventional MIPs. Further comparison is made with non-imprinted polymers (NIPs) that are based on cross-linking of pre-polymer units such as chitosan with epichlorohydrin in the absence of a molecular template. In general, MIPs offer the advantage of selectivity, chemical tunability, high stability and mechanical strength, ease of regeneration, and overall lower cost compared to NIPs. In particular, CD-MIPs offer the added advantage of possessing multiple binding sites with unique physicochemical properties such as tunable surface properties and morphology that may vary considerably. This mini-review provides a rationale for the design of unique polymer adsorbent materials that employ an intrinsic porogen via incorporation of a macrocyclic compound in the polymer framework to afford adsorbent materials with tunable physicochemical properties and unique nanostructure properties. PMID:28347047

Molecular dynamics simulation of the ionic liquid N-octylpyridinium tetrafluoroborate and acetonitrile: Thermodynamic and structural properties

NASA Astrophysics Data System (ADS)

Zhou, Siwen; Zhu, Guanglai; Kang, Xianqu; Li, Qiang; Sha, Maolin; Cui, Zhifeng; Xu, Xinsheng

2018-06-01

Using molecular dynamics simulation, the research obtained the thermodynamic properties and microstructures of the mixture of N-octylpyridinium tetrafluoroborate and acetonitrile, including density, self-diffusion coefficients, excess properties, radial distribution functions (RDFs) and spatial distribution functions (SDFs). Both RDFs and SDFs indicate that the local microstructure of the polar region is different from the nonpolar region with different mole fraction of ionic liquids. Acetonitrile could increase the order of the polar regions. While with acetonitrile increasing, the orderliness of the nonpolar region increases firstly and then decreases. In relatively dilute solution, ionic liquids were dispersed to form small aggregates wrapped by acetonitrile.

Pulse gas chromatographic study of adsorption of substituted aromatics and heterocyclic molecules on MIL-47 at zero coverage.

PubMed

Duerinck, Tim; Couck, Sarah; Vermoortele, Frederik; De Vos, Dirk E; Baron, Gino V; Denayer, Joeri F M

2012-10-02

The low coverage adsorptive properties of the MIL-47 metal organic framework toward aromatic and heterocyclic molecules are reported in this paper. The effect of molecular functionality and size on Henry adsorption constants and adsorption enthalpies of alkyl and heteroatom functionalized benzene derivates and heterocyclic molecules was studied using pulse gas chromatography. By means of statistical analysis, experimental data was analyzed and modeled using principal component analysis and partial least-squares regression. Structure-property relationships were established, revealing and confirming several trends. Among the molecular properties governing the adsorption process, vapor pressure, mean polarizability, and dipole moment play a determining role.

Effects of volumetric expansion in molecular crystals: A quantum mechanical investigation on aspirin and paracetamol most stable polymorphs

NASA Astrophysics Data System (ADS)

Adhikari, Kapil; Flurchick, Kenneth M.; Valenzano, Loredana

2015-02-01

This work reports a study performed at hybrid semi-empirical density functional level (B3LYP-D2*) of the physico-chemical properties of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) in their most stable crystalline forms. It is shown how effects arising from volumetric expansions influence the properties of the materials. Structural, energetic, and vibrational properties are in good agreement with experimental values reported at temperatures far from 0 K. Results show that the proposed approach is reliable enough to reproduce effects of volumetric expansion on lattice energies and other measurable physico-chemical observables related to inter-molecular forces.

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

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

Dunietz, Barry D

2016-08-09

The goal of the research program is to reliably describe electron transport and transfer processes at the molecular level. Such insight is essential for improving molecular applications of solar and thermal energy conversion. We develop electronic structure models to study (1) photoinduced electron transfer and transport processes in organic semiconducting materials, and (2) charge and heat transport through molecular bridges. We seek fundamental understanding of key processes, which lead to design new experiments and ultimately to achieve systems with improved properties.

Nonlinear optics of astaxanthin thin films

NASA Astrophysics Data System (ADS)

Esser, A.; Fisch, Herbert; Haas, Karl-Heinz; Haedicke, E.; Paust, J.; Schrof, Wolfgang; Ticktin, Anton

1993-02-01

Carotinoids exhibit large nonlinear optical properties due to their extended (pi) -electron system. Compared to other polyenes which show a broad distribution of conjugation lengths, carotinoids exhibit a well defined molecular structure, i.e. a well defined conjugation length. Therefore the carotinoid molecules can serve as model compounds to study the relationship between structure and nonlinear optical properties. In this paper the synthesis of four astaxanthins with C-numbers ranging from 30 to 60, their preparation into thin films, wavelength dispersive Third Harmonic Generation (THG) measurements and some molecular modelling calculations will be presented. Resonant (chi) (3) values reach 1.2(DOT)10-10 esu for C60 astaxanthin. In the nonresonant regime a figure of merit (chi) (3)/(alpha) of several 10-13 esu-cm is demonstrated.

Quantum molecular dynamics simulation of structural and thermodynamic properties of NiAl

NASA Astrophysics Data System (ADS)

Karchevskaya, E. S.; Minakov, D. V.; Levashov, P. R.

2018-01-01

In this work, structural and thermodynamic properties of a solid and liquid Ni-Al compound are studied using an ab initio method of quantum molecular dynamics (QMD). Simulations were carried out in 700-3000 K temperature range at atmospheric pressure. Radial distribution functions are analyzed to determine the presence of Ni-Al chemical bonds. Diffusion coefficients for individual components are also calculated. Another goal of this work is the investigation of the reaction propagation in thermally-initiated Ni-Al foils. For this purpose, we performed QMD simulations of Ni-Al layers in the microcanonical ensemble. An exothermic reaction between the solid Ni-Al layers is observed in our simulations at temperature less than the melting temperatures of the components.

Review on Abyssomicins: Inhibitors of the Chorismate Pathway and Folate Biosynthesis.

PubMed

Sadaka, Carmen; Ellsworth, Edmund; Hansen, Paul Robert; Ewin, Richard; Damborg, Peter; Watts, Jeffrey L

2018-06-06

Antifolates targeting folate biosynthesis within the shikimate-chorismate-folate metabolic pathway are ideal and selective antimicrobials, since higher eukaryotes lack this pathway and rely on an exogenous source of folate. Resistance to the available antifolates, inhibiting the folate pathway, underlines the need for novel antibiotic scaffolds and molecular targets. While para-aminobenzoic acid synthesis within the chorismate pathway constitutes a novel molecular target for antifolates, abyssomicins are its first known natural inhibitors. This review describes the abyssomicin family, a novel spirotetronate polyketide Class I antimicrobial. It summarizes synthetic and biological studies, structural, biosynthetic, and biological properties of the abyssomicin family members. This paper aims to explain their molecular target, mechanism of action, structure⁻activity relationship, and to explore their biological and pharmacological potential. Thirty-two natural abyssomicins and numerous synthetic analogues have been reported. The biological activity of abyssomicins includes their antimicrobial activity against Gram-positive bacteria and mycobacteria, antitumor properties, latent human immunodeficiency virus (HIV) reactivator, anti-HIV and HIV replication inducer properties. Their antimalarial properties have not been explored yet. Future analoging programs using the structure⁻activity relationship data and synthetic approaches may provide a novel abyssomicin structure that is active and devoid of cytotoxicity. Abyssomicin J and atrop- o -benzyl-desmethylabyssomicin C constitute promising candidates for such programs.

Effect of chitosan molecular weight on rheological behavious of chitosan modified nanoclay at highly hydrated state

USDA-ARS?s Scientific Manuscript database

Effect of chitosan molecular weight (M(cs)) on the rheological properties of chitosan modified clay (CMCs) at highly hydrated state was investigated. With special emphasis on its effect on the thixotropy of CMCs, the structure recovery at rest after underwent a pre-shearing process was further perfo...

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.

Crystal structure of channelrhodopsin, a light-gated cation channel – all cations lead through the monomer –

PubMed Central

Kato, Hideaki E.; Nureki, Osamu

2013-01-01

Channelrhodopsin (ChR) is a light-gated cation channel derived from green algae. Since the inward flow of cations triggers the neuron firing, neurons expressing ChRs can be optically controlled even within freely moving mammals. Although ChR has been broadly applied to neuro-science research, little is known about its molecular mechanisms. We determined the crystal structure of chimeric ChR at 2.3 Å resolution and revealed its molecular architecture. The integration of structural, electrophysio-logical, and computational analyses provided insight into the molecular basis for the channel function of ChR, and paved the way for the principled design of ChR variants with novel properties. PMID:27493541

Molecular-Level Control of Ciclopirox Olamine Release from Poly(ethylene oxide)-Based Mucoadhesive Buccal Films: Exploration of Structure-Property Relationships with Solid-State NMR.

PubMed

Urbanova, Martina; Gajdosova, Marketa; Steinhart, Miloš; Vetchy, David; Brus, Jiri

2016-05-02

Mucoadhesive buccal films (MBFs) provide an innovative way to facilitate the efficient site-specific delivery of active compounds while simultaneously separating the lesions from the environment of the oral cavity. The structural diversity of these complex multicomponent and mostly multiphase systems as well as an experimental strategy for their structural characterization at molecular scale with atomic resolution were demonstrated using MBFs of ciclopirox olamine (CPX) in a poly(ethylene oxide) (PEO) matrix as a case study. A detailed description of each component of the CPX/PEO films was followed by an analysis of the relationships between each component and the physicochemical properties of the MBFs. Two distinct MBFs were identified by solid-state NMR spectroscopy: (i) at low API (active pharmaceutical ingredient) loading, a nanoheterogeneous solid solution of CPX molecularly dispersed in an amorphous PEO matrix was created; and (ii) at high API loading, a pseudoco-crystalline system containing CPX-2-aminoethanol nanocrystals incorporated into the interlamellar space of a crystalline PEO matrix was revealed. These structural differences were found to be closely related to the mechanical and physicochemical properties of the prepared MBFs. At low API loading, the polymer chains of PEO provided sufficient quantities of binding sites to stabilize the CPX that was molecularly dispersed in the highly amorphous semiflexible polymer matrix. Consequently, the resulting MBFs were soft, with low tensile strength, plasticity, and swelling index, supporting rapid drug release. At high CPX content, however, the active compounds and the polymer chains simultaneously cocrystallized, leaving the CPX to form nanocrystals grown directly inside the spherulites of PEO. Interfacial polymer-drug interactions were thus responsible not only for the considerably enhanced plasticity of the system but also for the exclusive crystallization of CPX in the thermodynamically most stable polymorphic form, Form I, which exhibited reduced dissolution kinetics. The bioavailability of CPX olamine formulated as PEO-based MBFs can thus be effectively controlled by inducing the complete dispersion and/or microsegregation and nanocrystallization of CPX olamine in the polymer matrix. Solid-state NMR spectroscopy is an efficient tool for exploring structure-property relationships in these complex pharmaceutical solids.

CALCULATING PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FOR ENVIRONMENTAL MODELING FROM MOLECULAR STRUCTURE

EPA Science Inventory

Mathematical models for predicting the transport and fate of pollutants in the environment require reactivity parameter values-- that is value of the physical and chemical constants that govern reactivity. Although empirical structure activity relationships have been developed t...

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

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

Deichmann, Gregor; Marcon, Valentina; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived frommore » fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.« less

Investigation of thermal energy transport interface of hybrid graphene-carbon nanotube/polyethylene nanocomposites.

PubMed

Liu, Feng; Liu, Xuyang; Hu, Ning; Ning, Huiming; Atobe, Satoshi; Yan, Cheng; Mo, Fuhao; Fu, Shaoyun; Zhang, Jianyu; Wang, Yu; Mu, Xiaojing

2017-10-31

It is well known the thermal properties of three-dimensional (3-D) hybrid graphene (GR)-carbon nanotube (CNT) structures are not superior to that of the individual GR and CNT, however, the 3-D hybrid GR-CNT structures can effectively improve the thermal properties of polymer matrix. Therefore, understanding the thermal energy transport in the interface between polymer matrix and 3-D hybrid GR-CNT structure is essential. Here, the enhancement mechanism of interfacial thermal transport of hybrid GR-CNT structure was explored by applying non-equilibrium molecular dynamics (NEMD) simulations. Three different types of hybrid GR-CNT structures were built. The influences of CNT radius and CNT type for the hybrid GR-CNT on the interfacial thermal properties were also analyzed. Computational results show that among the three different types of hybrid GR-CNT structures, the Model-I, i.e., the covalent bond hybrid GR-CNT structures are of the best interfacial thermal properties. Meanwhile, the CNT radius of hybrid GR-CNT structure has a great influence on the interfacial thermal properties.

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.

On the history of the connectivity index: from the connectivity index to the exact solution of the protein alignment problem.

PubMed

Randić, M

2015-01-01

We briefly review the history of the connectivity index from 1975 to date. We hope to throw some light on why this unique, by its design, graph theoretical molecular descriptor continues to be of interest in QSAR, having wide use in applications in structure-property and structure-activity studies. We will elaborate on its generalizations and the insights it offered on applications in Multiple Regression Analysis (MRA). Going beyond the connectivity index we will outline several related developments in the development of molecular descriptors used in MRA, including molecular ID numbers (1986), the variable connectivity index (1991), orthogonal regression (1991), irrelevance of co-linearity of descriptors (1997), anti-connectivity (2006), and high discriminatory descriptors characterizing molecular similarity (2015). We will comment on beauty in QSAR and recent progress in searching for similarity of DNA, proteins and the proteome. This review reports on several results which are little known to the structure-property-activity community, the significance of which may surprise those unfamiliar with the application of discrete mathematics to chemistry. It tells the reader many unknown stories about the connectivity index, which may help the reader to better understand the meaning of this index. Readers are not required to be familiar with graph theory.

Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

NASA Astrophysics Data System (ADS)

Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

2018-03-01

Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

Dipicolinate salt of imidazole: Discovering its structure and properties using different experimental methodologies and quantum chemical investigations

NASA Astrophysics Data System (ADS)

Thirumurugan, R.; Anitha, K.

2018-03-01

A novel organic proton transfer complex of imidazolium dipicolinate (ID) has been synthesized and it was grown as single crystals using slow evaporation method. The molecular structure of synthesized compound and vibrational modes of its functional groups were confirmed by (1H and 13C) NMR, FTIR and FT-Raman spectroscopic studies, respectively. Single crystal X-ray diffraction (SCXRD) analysis confirmed the orthorhombic system with noncentrosymmetric (NCS), P212121, space group of grown ID crystal. UV-Vis-NIR spectral study confirmed its high optical transparency within the region of 285-1500 nm. Powder second harmonic generation (SHG) efficiency of ID crystal was confirmed and it was 6.8 times that of KDP crystal. TG-DTA and DSC analysis revealed the higher thermal stability of grown crystal as 249 °C. The dielectric response and mechanical behaviour of grown crystal were studied effectively. Density functional theory calculations were performed to probe the relationship between the structure and its properties including molecular optimization, Mulliken atomic charge distribution, frontier molecular orbital (FMOs) and molecular electrostatic potential map (MEP) analysis and first hyperpolarizability. All these experimental and computational results were discussed in this communication and it endorsed the ID compound as a potential NLO candidate could be employed in optoelectronics device applications in near future.

Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity.

PubMed

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites.

Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity

PubMed Central

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites. PMID:26442281

Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.

PubMed

Nakano, Miki; Watanabe, Hirofumi; Rothstein, Stuart M; Tanaka, Shigenori

2010-05-27

Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for alpha-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.

Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

PubMed

Shin, Sucheol; Willard, Adam P

2018-06-05

We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

Structure-activity relationships in beta-defensin peptides.

PubMed

Taylor, Karen; Barran, Perdita E; Dorin, Julia R

2008-01-01

The beta-defensins comprise a large family of small cationic antimicrobial peptides widely distributed in plants, mammals and insects. These cysteine rich peptides display multifunctional properties with implications as potential therapeutic agents. Recent research has highlighted their role in both the innate and adaptive immune systems as well as being novel melanocortin ligands. Studies investigating structure and function provide an insight into the molecular basis of their immunological properties. (c) 2007 Wiley Periodicals, Inc.

Theoretical insights into the effects of molar ratios on stabilities, mechanical properties, and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation.

PubMed

Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

2017-01-01

To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.

Structure and Li+ ion transport in a mixed carbonate/LiPF6 electrolyte near graphite electrode surfaces: a molecular dynamics study.

PubMed

Boyer, Mathew J; Vilčiauskas, Linas; Hwang, Gyeong S

2016-10-12

Electrolyte and electrode materials used in lithium-ion batteries have been studied separately to a great extent, however the structural and dynamical properties of the electrolyte-electrode interface still remain largely unexplored despite its critical role in governing battery performance. Using molecular dynamics simulations, we examine the structural reorganization of solvent molecules (cyclic ethylene carbonate : linear dimethyl carbonate 1 : 1 molar ratio doped with 1 M LiPF 6 ) in the vicinity of graphite electrodes with varying surface charge densities (σ). The interfacial structure is found to be sensitive to the molecular geometry and polarity of each solvent molecule as well as the surface structure and charge distribution of the negative electrode. We also evaluated the potential difference across the electrolyte-electrode interface, which exhibits a nearly linear variation with respect to σ up until the onset of Li + ion accumulation onto the graphite edges from the electrolyte. In addition, well-tempered metadynamics simulations are employed to predict the free-energy barriers to Li + ion transport through the relatively dense interfacial layer, along with analysis of the Li + solvation sheath structure. Quantitative analysis of the molecular arrangements at the electrolyte-electrode interface will help better understand and describe electrolyte decomposition, especially in the early stages of solid-electrolyte-interphase (SEI) formation. Moreover, the computational framework presented in this work offers a means to explore the effects of solvent composition, electrode surface modification, and operating temperature on the interfacial structure and properties, which may further assist in efforts to engineer the electrolyte-electrode interface leading to a SEI layer that optimizes battery performance.

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

DOE PAGES

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles; ...

2017-06-20

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

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

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations

PubMed Central

Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

2017-01-01

Tri-block copolymer styrene–butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG–DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as –OH, C=O, –COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds on the molecular structure of aged SBS. PMID:28773124

Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations.

PubMed

Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

2017-07-07

Tri-block copolymer styrene-butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG-DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as -OH, C=O, -COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds on the molecular structure of aged SBS.

Simulation studies on structural and thermal properties of alkane thiol capped gold nanoparticles.

PubMed

Devi, J Meena

2017-06-01

The structural and thermal properties of the passivated gold nanoparticles were explored employing molecular dynamics simulation for the different surface coverage densities of the self-assembled monolayer (SAM) of alkane thiol. The structural properties of the monolayer protected gold nanoparticles such us overall shape, organization and conformation of the capping alkane thiol chains were found to be influenced by the capping density. The structural order of the thiol capped gold nanoparticles enhances with the increase in the surface coverage density. The specific heat capacity of the alkane thiol capped gold nanoparticles was found to increase linearly with the thiol coverage density. This may be attributed to the enhancement in the lattice vibrational energy. The present simulation results suggest, that the structural and thermal properties of the alkane thiol capped gold nanoparticles may be modified by the suitable selection of the SAM coverage density. Copyright © 2017 Elsevier Inc. All rights reserved.

Demystifying Mechanosensitive Piezo Ion Channels.

PubMed

Xu, X Z Shawn

2016-06-01

Mechanosensitive channels mediate touch, hearing, proprioception, and blood pressure regulation. Piezo proteins, including Piezo1 and Piezo2, represent a new class of mechanosensitive channels that have been reported to play key roles in most, if not all, of these modalities. The structural architecture and molecular mechanisms by which Piezos act as mechanosensitive channels, however, remain mysterious. Two new studies have now provided critical insights into the atomic structure and molecular basis of the ion permeation and mechano-gating properties of the Piezo1 channel.

First-principles molecular dynamics simulation study on electrolytes for use in redox flow battery

NASA Astrophysics Data System (ADS)

Choe, Yoong-Kee; Tsuchida, Eiji; Tokuda, Kazuya; Ootsuka, Jun; Saito, Yoshihiro; Masuno, Atsunobu; Inoue, Hiroyuki

2017-11-01

Results of first-principles molecular dynamics simulations carried out to investigate structural aspects of electrolytes for use in a redox flow battery are reported. The electrolytes studied here are aqueous sulfuric acid solutions where its property is of importance for dissolving redox couples in redox flow battery. The simulation results indicate that structural features of the acid solutions depend on the concentration of sulfuric acid. Such dependency arises from increase of proton dissociation from sulfuric acid.

Growth of Y3Fe5O12/GaN layers by laser molecular-beam epitaxy and characterization of their structural and magnetic properties

NASA Astrophysics Data System (ADS)

Kaveev, A. K.; Bursian, V. E.; Gastev, S. V.; Krichevtsov, B. B.; Suturin, S. M.; Volkov, M. P.; Sokolov, N. S.

2016-12-01

Laser molecular-beam epitaxy has been employed to obtain layers of yttrium-iron garnet (YIG) Y3Fe5O12 on gallium nitride substrates. It was found that there exists a polycrystalline YIG phase without admixtures of other structural phases. A magnetic anisotropy of films of the "easy-magnetic plane" type was found. The gyromagnetic ratio and the demagnetizing field 4π M S were calculated.

Structures and Optical Properties of Hydrazones Derived from Biological Polyenes

NASA Astrophysics Data System (ADS)

Nakashima, Takayasu; Yamada, Takashi; Hashimoto, Hideki; Kobayashi, Takayoshi

2001-08-01

A set of hydrazone molecules was derived from a series of biological polyenes that have different polyene chain-lengths with common substituent group of 2,4-dinitrophenylhydrazine. Their structures were determined by high-resolution NMR spectroscopy as well as X-ray crystallography, and their optical properties were investigated by room and low temperature optical absorption spectroscopy. Among the derivatives so far synthesized, the one that has the shortest polyene chain (C13-DNPH) afforded single crystals without inversion symmetry, hence applicable for the second-order nonlinear optical devices. Molecular structures in the crystals were closely inspected in order to explain the cause to violate the inversion symmetry. Hydrazones derived in this study gave rise to two transition moments along the molecular axis. Comparison of the optical absorption spectra among the derivatives showed a unique phenomenon that could be attributed to the crossover of the excited state potential energy surfaces along the elongation of the polyene chain-lengths.

Structures and Optical Properties of Hydrazones Derived from Biological Polyenes

NASA Astrophysics Data System (ADS)

Nakashima, Takayasu; Yamada, Takashi; Hashimoto, Hideki; Kobayashi, Takayoshi

A set of hydrazone molecules was derived from a series of biological polyenes that have different polyene chain-lengths with common substituent group of 2,4-dinitrophenylhydrazine. Their structures were determined by high-resolution NMR spectroscopy as well as X-ray crystallography, and their optical properties were investigated by room and low temperature optical absorption spectroscopy. Among the derivatives so far synthesized, the one that has the shortest polyene chain (C13-DNPH) afforded single crystals without inversion symmetry, hence applicable for the second-order nonlinear optical devices. Molecular structures in the crystals were closely inspected in order to explain the cause to violate the inversion symmetry. Hydrazones derived in this study gave rise to two transition moments along the molecular axis. Comparison of the optical absorption spectra among the derivatives showed a unique phenomenon that could be attributed to the crossover of the excited state potential energy surfaces along the elongation of the polyene chain-lengths.

Quantum chemical study of small AlnBm clusters: Structure and physical properties

NASA Astrophysics Data System (ADS)

Loukhovitski, Boris I.; Sharipov, Alexander S.; Starik, Alexander M.

2017-08-01

The structure and physical properties, including rotational constants, characteristic vibrational temperatures, collision diameter, dipole moment, static polarizability, the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), and formation enthalpy of the different isomeric forms of AlnBm clusters with n + m ⩽ 7 are studied using density functional theory. The search of the structure of isomers has been carried employing multistep hierarchical algorithm. Temperature dependencies of thermodynamic functions, such as enthalpy, entropy, and specific heat capacity, have been determined both for the individual isomers and for the ensembles with equilibrium and frozen compositions for the each class of clusters taking into account the anharmonicity of cluster vibrations and the contribution of their excited electronic states. The prospects of the application of small AlnBm clusters as the components of energetic materials are also considered.

Blueberries and Tofu: Friend or Foe?

NASA Astrophysics Data System (ADS)

D'Ascoli, Jennifer; Lee, Susanne

2004-03-01

Two flavonoids, naringenin and genistein found in blueberries and soybeans, respectively, scavenge free radicals and exhibit anti- breast and prostate cancer properties. When consumed in foods, these flavonoids usually are subject to heat, yet all biological studies have been performed with unheated molecules. We have explored and will report on the three-dimensional, molecular structure changes we have thermally-induced in naringenin and genistein. We have measured and will discuss the flavonoids' thermodynamic properties as a function of temperature. Several endothermic transformations were observed along with a marked color change that remained when the flavonoids were dissolved in a solvent, indicating their molecular structures had been altered by the heat. Ultraviolet-Visible spectroscopy, and proton and carbon 1-D nuclear magnetic resonance will be presented that show the change was associated with a decrease in electron localization within the molecules. We will explain how such modified structures could scavenge free radicals more effectively and affect breast cancer cell proliferation.

Biosynthesis, structural architecture and biotechnological potential of bacterial tannase: a molecular advancement.

PubMed

Jana, Arijit; Halder, Suman Kumar; Banerjee, Amrita; Paul, Tanmay; Pati, Bikash Ranjan; Mondal, Keshab Chandra; Das Mohapatra, Pradeep Kumar

2014-04-01

Tannin-rich materials are abundantly generated as wastes from several agroindustrial activities. Therefore, tannase is an interesting hydrolase, for bioconversion of tannin-rich materials into value added products by catalyzing the hydrolysis of ester and depside bonds and unlocked a new prospect in different industrial sectors like food, beverages, pharmaceuticals, etc. Microorganisms, particularly bacteria are one of the major sources of tannase. In the last decade, cloning and heterologous expression of novel tannase genes and structural study has gained momentum. In this article, we have emphasized critically on bacterial tannase that have gained worldwide research interest for their diverse properties. The present paper delineate the developments that have taken place in understanding the role of tannase action, microbial sources, various cultivation aspects, downstream processing, salient biochemical properties, structure and active sites, immobilization, efforts in cloning and overexpression and with special emphasis on recent molecular and biotechnological achievements. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

The influence of electron-beam irradiation on the chemical and the structural properties of medical-grade polyurethane

NASA Astrophysics Data System (ADS)

Shin, Sukyoung; Lee, Soonhyouk

2015-07-01

Thermo plastic polyurethane (TPU) provides excellent bio-compatibility, flexibility and good irradiation resistance; however, extremely high irradiation doses can alter the structure and the function of macromolecules, resulting in oxidation, chain scission and cross-linking. In this study, the effects of e-beam irradiation on the medical-grade thermo plastic polyurethane were studied. Changes in the chain length and their distribution, as well as changes in the molecular structure were studied. The GPC (gel permeation chromatography) results show that the oxidative decomposition is followed by a decrease in the molecular mass and an increase in polydispersity. This indicates a very inhomogeneous degradation, which is a consequence of the specific course and of the intensity of oxidative degradation. This was confirmed by means of mechanical property measurements. Overall, this study demonstrated that medical-grade TPU was affected by radiation exposure, particularly at high irradiation doses.

Combined experimental and theoretical studies on the molecular structures, spectroscopy, and inhibitor activity of 3-(2-thienyl)acrylic acid through AIM, NBO,FT-IR, FT-Raman, UV and HOMO-LUMO analyses, and molecular docking

NASA Astrophysics Data System (ADS)

Issaoui, N.; Ghalla, H.; Bardak, F.; Karabacak, M.; Aouled Dlala, N.; Flakus, H. T.; Oujia, B.

2017-02-01

In this work, the molecular structures and vibrational spectral analyses of 3-(2-Theinyl)acrylic acid (3-2TAA) monomer and dimer structures have been reported by using density functional theory calculations at B3LYP/6-311++G(d,p) level of theory. The complete assignments of the fundamental vibrational modes were obtained using potential energy distribution. Intermolecular interactions were analyzed by orbital NBO and topological AIM approaches. The electronic properties have been carried out using TD-DFT approach. Great agreements between experimental and theoretical values were achieved throughout the analysis of structural parameters and spectroscopic features. Inhibitor characteristics on human monoamine oxidase B (MAOB) enzyme of two determined stable conformers of 3-2TAA (β and γ) along with four selective inhibitors, namely safinamide, a coumarin analogue, farnesol, and phenyethylhydrazine were investigated via molecular docking. Moreover, molecular electrostatic potential (MEP) and temperature dependency of thermodynamic functions have been reported.

Assessment of the electronic structure and properties of trichothecene toxins using density functional theory

USDA-ARS?s Scientific Manuscript database

A comprehensive quantum chemical study was carried out on 34 type A and type B trichothecenes, including selected derivatives and biosynthetic precursors of deoxynivalenol, nivalenol, and T-2 toxin. Quantum parameters, Natural Bond Orbital (NBO) analysis, and molecular properties were calculated on ...

Self-assembly of conjugated oligomers and polymers at the interface: structure and properties.

PubMed

Xu, Lirong; Yang, Liu; Lei, Shengbin

2012-08-07

In this review, we give a brief account on the recent scanning tunneling microscopy investigation of interfacial structures and properties of π-conjugated semiconducting oligomers and polymers, either at the solid-air (including solid-vacuum) or at the solid-liquid interface. The structural aspects of the self-assembly of both oligomers and polymers are highlighted. Conjugated oligomers can form well ordered supramolecular assemblies either at the air-solid or liquid-solid interface, thanks to the relatively high mobility and structural uniformity in comparison with polymers. The backbone structure, substitution of side chains and functional groups can affect the assembling behavior significantly, which offers the opportunity to tune the supramolecular structure of these conjugated oligomers at the interface. For conjugated polymers, the large molecular weight limits the mobility on the surface and the distribution in size also prevents the formation of long range ordered supramolecular assembly. The submolecular resolution obtained on the assembling monolayers enables a detailed investigation of the chain folding at the interface, both the structural details and the effect on electronic properties. Besides the ability in studying the assembling structures at the interfaces, STM also provides a reasonable way to evaluate the distribution of the molecular weight of conjugated polymers by statistic of the contour length of the adsorbed polymer chains. Both conjugated oligomers and polymers can form composite assemblies with other materials. The ordered assembly of oligomers can act as a template to controllably disperse other molecules such as coronene or fullerene. These investigations open a new avenue to fine tune the assembling structure at the interface and in turn the properties of the composite materials. To summarize scanning tunneling microscopy has demonstrated its surprising ability in the investigation of the assembling structures and properties of conjugated oligomers and polymers. The information obtained could benefit the understanding of the elements affecting the film morphology and helps the optimization of device performance.

Building better water models using the shape of the charge distribution of a water molecule

NASA Astrophysics Data System (ADS)

Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko

2017-11-01

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

Application of Generative Autoencoder in De Novo Molecular Design.

PubMed

Blaschke, Thomas; Olivecrona, Marcus; Engkvist, Ola; Bajorath, Jürgen; Chen, Hongming

2018-01-01

A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning methodology, for de novo molecular design. Various generative autoencoders were used to map molecule structures into a continuous latent space and vice versa and their performance as structure generator was assessed. Our results show that the latent space preserves chemical similarity principle and thus can be used for the generation of analogue structures. Furthermore, the latent space created by autoencoders were searched systematically to generate novel compounds with predicted activity against dopamine receptor type 2 and compounds similar to known active compounds not included in the trainings set were identified. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires. Using quantum-based calculations, we modeled 'p-type' polaron transport through oligophenylenethiophene (OPTI) wires and assigned transport activation energies to specific modes of nuclear motion. We also show control over 'n-type', LUMO-mediated transport in short ( 2 nm) redox-active perylenediimide (PDI) SAMs bound to contacts through isocyano linkers. By changing the contact work function (φ) and temperature, we were able to verify thermally-assisted LUMO transport. Transition voltage spectroscopy and the single level model was employed to fit the experimental I-V curves and extract the electronic coupling (epsilon) and the EF-LUMO offset (epsilonl). It was found that epsilonl does not change with φ (LUMO pinning), while Gamma changes with both φ and temperature. Further, the PDI SAMs could be reversibly chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

Structural adaptation of the subunit interface of oligomeric thermophilic and hyperthermophilic enzymes.

PubMed

Maugini, Elisa; Tronelli, Daniele; Bossa, Francesco; Pascarella, Stefano

2009-04-01

Enzymes from thermophilic and, particularly, from hyperthermophilic organisms are surprisingly stable. Understanding of the molecular origin of protein thermostability and thermoactivity attracted the interest of many scientist both for the perspective comprehension of the principles of protein structure and for the possible biotechnological applications through application of protein engineering. Comparative studies at sequence and structure levels were aimed at detecting significant differences of structural parameters related to protein stability between thermophilic and hyperhermophilic structures and their mesophilic homologs. Comparative studies were useful in the identification of a few recurrent themes which the evolution utilized in different combinations in different protein families. These studies were mostly carried out at the monomer level. However, maintenance of a proper quaternary structure is an essential prerequisite for a functional macromolecule. At the environmental temperatures experienced typically by hyper- and thermophiles, the subunit interactions mediated by the interface must be sufficiently stable. Our analysis was therefore aimed at the identification of the molecular strategies adopted by evolution to enhance interface thermostability of oligomeric enzymes. The variation of several structural properties related to protein stability were tested at the subunit interfaces of thermophilic and hyperthermophilic oligomers. The differences of the interface structural features observed between the hyperthermophilic and thermophilic enzymes were compared with the differences of the same properties calculated from pairwise comparisons of oligomeric mesophilic proteins contained in a reference dataset. The significance of the observed differences of structural properties was measured by a t-test. Ion pairs and hydrogen bonds do not vary significantly while hydrophobic contact area increases specially in hyperthermophilic interfaces. Interface compactness also appears to increase in the hyperthermophilic proteins. Variations of amino acid composition at the interfaces reflects the variation of the interface properties.

Superconducting selenides intercalated with organic molecules: synthesis, crystal structure, electric and magnetic properties, superconducting properties, and phase separation in iron based-chalcogenides and hybrid organic-inorganic superconductors

NASA Astrophysics Data System (ADS)

Krzton-Maziopa, Anna; Pesko, Edyta; Puzniak, Roman

2018-06-01

Layered iron-based superconducting chalcogenides intercalated with molecular species are the subject of intensive studies, especially in the field of solid state chemistry and condensed matter physics, because of their intriguing chemistry and tunable electric and magnetic properties. Considerable progress in the research, revealing superconducting inorganic–organic hybrid materials with transition temperatures to superconducting state, T c, up to 46 K, has been brought in recent years. These novel materials are synthesized by low-temperature intercalation of molecular species, such as solvates of alkali metals and nitrogen-containing donor compounds, into layered FeSe-type structure. Both the chemical nature as well as orientation of organic molecules between the layers of inorganic host, play an important role in structural modifications and may be used for fine tuning of superconducting properties. Furthermore, a variety of donor species compatible with alkali metals, as well as the possibility of doping also in the host structure (either on Fe or Se sites), makes this system quite flexible and gives a vast array of new materials with tunable electric and magnetic properties. In this review, the main aspects of intercalation chemistry are discussed with a particular attention paid to the influence of the unique nature of intercalating species on the crystal structure and physical properties of the hybrid inorganic–organic materials. To get a full picture of these materials, a comprehensive description of the most effective chemical and electrochemical methods, utilized for synthesis of intercalated species, with critical evaluation of their strong and weak points, related to feasibility of synthesis, phase purity, crystal size and morphology of final products, is included as well.

Fibrin mechanical properties and their structural origins.

PubMed

Litvinov, Rustem I; Weisel, John W

2017-07-01

Fibrin is a protein polymer that is essential for hemostasis and thrombosis, wound healing, and several other biological functions and pathological conditions that involve extracellular matrix. In addition to molecular and cellular interactions, fibrin mechanics has been recently shown to underlie clot behavior in the highly dynamic intra- and extravascular environments. Fibrin has both elastic and viscous properties. Perhaps the most remarkable rheological feature of the fibrin network is an extremely high elasticity and stability despite very low protein content. Another important mechanical property that is common to many filamentous protein polymers but not other polymers is stiffening occurring in response to shear, tension, or compression. New data has begun to provide a structural basis for the unique mechanical behavior of fibrin that originates from its complex multi-scale hierarchical structure. The mechanical behavior of the whole fibrin gel is governed largely by the properties of single fibers and their ensembles, including changes in fiber orientation, stretching, bending, and buckling. The properties of individual fibrin fibers are determined by the number and packing arrangements of double-stranded half-staggered protofibrils, which still remain poorly understood. It has also been proposed that forced unfolding of sub-molecular structures, including elongation of flexible and relatively unstructured portions of fibrin molecules, can contribute to fibrin deformations. In spite of a great increase in our knowledge of the structural mechanics of fibrin, much about the mechanisms of fibrin's biological functions remains unknown. Fibrin deformability is not only an essential part of the biomechanics of hemostasis and thrombosis, but also a rapidly developing field of bioengineering that uses fibrin as a versatile biomaterial with exceptional and tunable biochemical and mechanical properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Negative differential resistance and switch behavior of T-BxNy (x, y = 5, 6, 11) molecular junctions

NASA Astrophysics Data System (ADS)

Wang, Shi-Liang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Xin, Jian-Guo

2017-05-01

The electronic transport properties of T-BxNy (x, y = 5, 6, 11) molecular junction are investigated based on first-principle density functional theory and non-equilibrium Green's function method. Strong negative differential resistance (NDR) behavior is observed for T-B5N6 molecule under negative and positive bias voltages, with an obvious switch effect for T-B6N5. However, only small NDR is shown for the complex of the two molecules. The projected device density of states, the spatial distribution of molecular orbitals, and the effect of transmission spectra under various bias voltages on the electronic transport properties are analyzed. The obvious effect of bias voltage on the changes in the electronic distribution of frontier molecular orbitals is responsible for the NDR or switch behavior. Therefore, different functional molecular devices can be obtained with different structures of T-BxNy.

A SAR and QSAR study of new artemisinin compounds with antimalarial activity.

PubMed

Santos, Cleydson Breno R; Vieira, Josinete B; Lobato, Cleison C; Hage-Melim, Lorane I S; Souto, Raimundo N P; Lima, Clarissa S; Costa, Elizabeth V M; Brasil, Davi S B; Macêdo, Williams Jorge C; Carvalho, José Carlos T

2013-12-30

The Hartree-Fock method and the 6-31G** basis set were employed to calculate the molecular properties of artemisinin and 20 derivatives with antimalarial activity. Maps of molecular electrostatic potential (MEPs) and molecular docking were used to investigate the interaction between ligands and the receptor (heme). Principal component analysis and hierarchical cluster analysis were employed to select the most important descriptors related to activity. The correlation between biological activity and molecular properties was obtained using the partial least squares and principal component regression methods. The regression PLS and PCR models built in this study were also used to predict the antimalarial activity of 30 new artemisinin compounds with unknown activity. The models obtained showed not only statistical significance but also predictive ability. The significant molecular descriptors related to the compounds with antimalarial activity were the hydration energy (HE), the charge on the O11 oxygen atom (QO11), the torsion angle O1-O2-Fe-N2 (D2) and the maximum rate of R/Sanderson Electronegativity (RTe+). These variables led to a physical and structural explanation of the molecular properties that should be selected for when designing new ligands to be used as antimalarial agents.

Bayesian molecular design with a chemical language model

NASA Astrophysics Data System (ADS)

Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

2017-04-01

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

Bayesian molecular design with a chemical language model.

PubMed

Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

2017-04-01

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

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.

Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein.

PubMed Central

Pastor, N; Pardo, L; Weinstein, H

1997-01-01

The binding of the TATA box-binding protein (TBP) to a TATA sequence in DNA is essential for eukaryotic basal transcription. TBP binds in the minor groove of DNA, causing a large distortion of the DNA helix. Given the apparent stereochemical equivalence of AT and TA basepairs in the minor groove, DNA deformability must play a significant role in binding site selection, because not all AT-rich sequences are bound effectively by TBP. To gain insight into the precise role that the properties of the TATA sequence have in determining the specificity of the DNA substrates of TBP, the solution structure and dynamics of seven DNA dodecamers have been studied by using molecular dynamics simulations. The analysis of the structural properties of basepair steps in these TATA sequences suggests a reason for the preference for alternating pyrimidine-purine (YR) sequences, but indicates that these properties cannot be the sole determinant of the sequence specificity of TBP. Rather, recognition depends on the interplay between the inherent deformability of the DNA and steric complementarity at the molecular interface. Images FIGURE 2 PMID:9251783

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.

Magnetic behavior in Cr{sub 2}@Ge{sub n} (1≤n≤12) clusters: A density functional investigation

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

Dhaka, Kapil, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in; Trivedi, Ravi, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in; Bandyopadhyay, Debashis, E-mail: kapil.dhaka@pilani.bits-pilani.ac.in

2014-04-24

With a goal to produce magnetic moment in Cr{sub 2} Doped Ge{sub n} clusters which will be useful for practical applications, we have considered the structure and magnetic properties of Pure Germanium clusters and substitutionally doped it with Cr dimer to produce Cr{sub 2}@Ge{sub n} clusters. As the first step of calculation, geometrical optimizations of the nanoclusters have been done. These optimized geometries have been used in calculate the average binding energy per atom (BE), HOMO-LUMO gap and hence the relative stability of the clusters. These parameters have been demonstrated as structural and electronic properties of the clusters. Gap betweenmore » highest occupied molecular orbital and lowest unoccupied molecular orbital indicate cluster to be a potential motif for generating magnetic cluster assembled materials. Based on these values a comparative study on different sized clusters has been done in order to understand the origin of structures, electronic and magnetic properties of Cr{sub 2}@Ge{sub n} nanoclusters.« less

Vibrational, spectroscopic, molecular docking and density functional theory studies on N-(5-aminopyridin-2-yl)acetamide

NASA Astrophysics Data System (ADS)

Asath, R. Mohamed; Rekha, T. N.; Premkumar, S.; Mathavan, T.; Benial, A. Milton Franklin

2016-12-01

Conformational analysis was carried out for N-(5-aminopyridin-2-yl)acetamide (APA) molecule. The most stable, optimized structure was predicted by the density functional theory calculations using the B3LYP functional with cc-pVQZ basis set. The optimized structural parameters and vibrational frequencies were calculated. The experimental and theoretical vibrational frequencies were assigned and compared. Ultraviolet-visible spectrum was simulated and validated experimentally. The molecular electrostatic potential surface was simulated. Frontier molecular orbitals and related molecular properties were computed, which reveals that the higher molecular reactivity and stability of the APA molecule and further density of states spectrum was simulated. The natural bond orbital analysis was also performed to confirm the bioactivity of the APA molecule. Antidiabetic activity was studied based on the molecular docking analysis and the APA molecule was identified that it can act as a good inhibitor against diabetic nephropathy.

Acetylcholine-Like Molecular Arrangement in Psychomimetic Anticholinergic Drugs

PubMed Central

Maayani, Saul; Weinstein, Harel; Cohen, Sasson; Sokolovsky, Mordechai

1973-01-01

A study of the relation between the psychotropic activity and the antagonism to acetylcholine observed for some heterocyclic amino esters and compounds of the phencyclidine series suggests some common molecular structural requirements for their properties. Criteria obtained from quantum mechanical calculations of acetylcholine-like molecules indicate that their molecular reactivity with the cholinergic receptor site follows a certain dynamic interaction pattern. This pattern suggests a certain molecular arrangement essential for the interaction, which is based on the electronic properties of the molecules and therefore remains valid for the evaluation of compounds which lack any apparent similarity to acetylcholine. This type of molecular arrangement is shown to be shared by both activators and inhibitors of the acetylcholine receptor discussed here, thus supporting the hypothesis of their binding to a common receptor. The differences in biological activity are attributed to the effect of molecular structural factors which are not commonly included in the molecular arrangement based on the active groups of acetylcholine. The role of such factors is revealed by a study of the observed differences in the cholinergic and psychomimetic activities of related pairs of isomers and enantiomers of the molecules investigated. Structural factors which interfere with the conformational changes occurring in the receptor protein induced by an activator are characterized through differences obtained by the comparative investigation of the activities of the agonist acetate and the antagonist benzilate amino esters of quinuclidine, tropine, and pseudotropine. The same factors are shown in studies of the phencyclidine series to contribute to the antagonism to acetylcholine activity that is closely related to the psychomimetic activity of these drugs in the central nervous system. Similarly, phencyclidine derivatives in which the characteristic acetylcholine-like molecular arrangement is modified by various substitutions are shown to loose both anticholinergic and psychotropic behavior. This close correlation is supported by the identification of molecular regions which will generate the proper molecular arrangement in local anesthetics and morphine, compounds which are known to be involved in cholinergic mechanisms. Images PMID:4522291

The simulation of molecular clouds formation in the Milky Way

NASA Astrophysics Data System (ADS)

Khoperskov, S. A.; Vasiliev, E. O.; Sobolev, A. M.; Khoperskov, A. V.

2013-01-01

Using 3D hydrodynamic calculations we simulate formation of molecular clouds in the Galaxy. The simulations take into account molecular hydrogen chemical kinetics, cooling and heating processes. Comprehensive gravitational potential accounts for contributions from the stellar bulge, two- and four-armed spiral structure, stellar disc, dark halo and takes into account self-gravitation of the gaseous component. Gas clouds in our model form in the spiral arms due to shear and wiggle instabilities and turn into molecular clouds after t ≳ 100 Myr. At the times t ˜ 100-300 Myr the clouds form hierarchical structures and agglomerations with the sizes of 100 pc and greater. We analyse physical properties of the simulated clouds and find that synthetic statistical distributions like mass spectrum, `mass-size' relation and velocity dispersion are close to those observed in the Galaxy. The synthetic l-v (galactic longitude-radial velocity) diagram of the simulated molecular gas distribution resembles observed one and displays a structure with appearance similar to molecular ring of the Galaxy. Existence of this structure in our modelling can be explained by superposition of emission from the galactic bar and the spiral arms at ˜3-4 kpc.

A theoretical study of molecular structure, optical properties and bond activation of energetic compound FOX-7 under intense electric fields

NASA Astrophysics Data System (ADS)

Tao, Zhiqiang; Wang, Xin; Wei, Yuan; Lv, Li; Wu, Deyin; Yang, Mingli

2017-02-01

Molecular structure, vibrational and electronic absorption spectra, chemical reactivity of energetic compound FOX-7, one of the most widely used explosives, were studied computationally in presence of an electrostatic field of 0.01-0.05 a.u. The Csbnd N bond, which usually triggers the decomposition of FOX-7, is shortened/elongated under a parallel/antiparallel field. The Csbnd N bond activation energy varies with the external electric field, decreasing remarkably with the field strength in regardless of the field direction. This is attributed to two aspects: the bond weakening by the field parallel to the Csbnd N bond and the stabilization effect on the transition-state structure by the field antiparallel to the bond. The variations in the structure and property of FOX-7 under the electric fields were further analyzed with its distributional polarizability, which is dependent on the charge transfer characteristics through the Csbnd N bond.

Influence of the extraction process on the rheological and structural properties of agars.

PubMed

Sousa, Ana M M; Borges, João; Silva, A Fernando; Gonçalves, Maria P

2013-07-01

Agars obtained by traditional hot-water (TWE) and microwave-assisted (MAE) extractions were compared in terms of their rheological and physicochemical properties and molecular self-association in solutions of low (0.05%, w/w) and high (1.5%, w/w) polymer concentrations. At low concentration, thin gelled layers were imaged by AFM. Slow or rapid cooling of the solutions influenced structure formation. In each case, TWE and MAE agar structures were different and apparently larger for MAE. At high concentration, progressive structural reinforcement was seen; while TWE agar showed a more open and irregular 3D network, MAE agar gel imaged by cryoSEM was denser and fairly uniform. The rheological (higher thermal stability and consistency) and mechanical (higher gel strength) behaviors of MAE agar seemed consistent with a positive effect of molecular mass and 3,6-anhydro-α-l-galactose content. MAE produced non-degraded agar comparable with commercial ones and if properly monitored, could be a promising alternative to TWE. Copyright © 2013 Elsevier Ltd. All rights reserved.

Interfacial assembly structures and nanotribological properties of saccharic acids.

PubMed

Shi, Hongyu; Liu, Yuhong; Zeng, Qingdao; Yang, Yanlian; Wang, Chen; Lu, Xinchun

2017-01-04

Saccharides have been recognized as potential bio-lubricants because of their good hydration ability. However, the interfacial structures of saccharides and their derivatives are rarely studied and the molecular details of interaction mechanisms have not been well understood. In this paper, the supramolecular assembly structures of saccharic acids (including galactaric acid and lactobionic acid), mediated by hydrogen bonds O-HN and O-HO, were successfully constructed on a highly oriented pyrolytic graphite (HOPG) surface by introducing pyridine modulators and were explicitly revealed by using scanning tunneling microscopy (STM). Furthermore, friction forces were measured in the saccharic acid/pyridine co-assembled system by atomic force microscopy (AFM), revealing a larger value than a pristine saccharic acid system, which could be attributed to the stronger tip-assembled molecule interactions that lead to the higher potential energy barrier needed to overcome. The effort on saccharide-related supramolecular self-assembly and nanotribological behavior could provide a novel and promising pathway to explore the interaction mechanisms underlying friction and reveal the structure-property relationship at the molecular level.

Tetrametallic molecular catalysts for photochemical water oxidation.

PubMed

Sartorel, Andrea; Bonchio, Marcella; Campagna, Sebastiano; Scandola, Franco

2013-03-21

Among molecular water oxidation catalysts (WOCs), those featuring a reactive set of four multi-redox transition metals can leverage an extraordinary interplay of electronic and structural properties. These are of particular interest, owing to their close structural, and possibly functional, relationship to the oxygen evolving complex of natural photosynthesis. In this review, special attention is given to two classes of tetrametallic molecular WOCs: (i) M(4)O(4) cubane-type structures stabilized by simple organic ligands, and (ii) systems in which a tetranuclear metal core is stabilized by coordination of two polyoxometalate (POM) ligands. Recent work in this rapidly evolving field is reviewed, with particular emphasis on photocatalytic aspects. Special attention is given to studies addressing the mechanistic complexity of these systems, sometimes overlooked in the rush for oxygen evolving performance. The complementary role of molecular WOCs and their relationship with bulk oxides and heterogeneous catalysis are discussed.

Structure-activity relationship of the ionic cocrystal: 5-amino-2-naphthalene sulfonate·ammonium ions for pharmaceutical applications

NASA Astrophysics Data System (ADS)

Sangeetha, M.; Mathammal, R.

2018-02-01

The ionic cocrystals of 5-amino-2-naphthalene sulfonate · ammonium ions (ANSA-ṡNH4+) were grown under slow evaporation method and examined in detail for pharmaceutical applications. The crystal structure and intermolecular interactions were studied from the single X-ray diffraction analysis and the Hirshfeld surfaces. The 2D fingerprint plots displayed the inter-contacts possible in the ionic crystal. Computational DFT method was established to determine the structural, physical and chemical properties. The molecular geometries obtained from the X-ray studies were compared with the optimized geometrical parameters calculated using DFT/6-31 + G(d,p) method. The band gap energy calculated from the UV-Visible spectral analysis and the HOMO-LUMO energy gap are compared. The theoretical UV-Visible calculations helped in determining the type of electronic transition taking place in the title molecule. The maximum absorption bands and transitions involved in the molecule represented the drug reaction possible. Non-linear optical properties were characterized from SHG efficiency measurements experimentally and the NLO parameters are also calculated from the optimized structure. The reactive sites within the molecule are detailed from the MEP surface maps. The molecular docking studies evident the structure-activity of the ionic cocrystal for anti-cancer drug property.

Rheological Properties of Gels from Pyrene Based Low Molecular Weight Gelators

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

Leivo, Kimmo T.; Hahma, Arno P.

2008-07-07

Gels of pyrene derived low molecular weight organogelators (LMOGs) in primary alcohols have been characterized by rheometry and scanning electron microscopy. Total gelator concentration was 1-2.7 % w/w depending on the solvent and the gelator, including equimolar amounts of the gelator and 2,4,7-trinitrofluorenone (TNF), which is necessary for gelation. Thermoreversible and strongly shear thinning gels were achieved as the two components interact non-covalently to form a gel network. A qualitative correlation between the rheological properties and the nanoscale gel structure were found.

Rheological Properties of Gels from Pyrene Based Low Molecular Weight Gelators

NASA Astrophysics Data System (ADS)

Leivo, Kimmo T.; Hahma, Arno P.

2008-07-01

Gels of pyrene derived low molecular weight organogelators (LMOGs) in primary alcohols have been characterized by rheometry and scanning electron microscopy. Total gelator concentration was 1-2.7 % w/w depending on the solvent and the gelator, including equimolar amounts of the gelator and 2,4,7-trinitrofluorenone (TNF), which is necessary for gelation. Thermoreversible and strongly shear thinning gels were achieved as the two components interact non-covalently to form a gel network. A qualitative correlation between the rheological properties and the nanoscale gel structure were found.

Complex basis functions for molecular resonances: Methodology and applications

NASA Astrophysics Data System (ADS)

White, Alec; McCurdy, C. William; Head-Gordon, Martin

The computation of positions and widths of metastable electronic states is a challenge for molecular electronic structure theory because, in addition to the difficulty of the many-body problem, such states obey scattering boundary conditions. These resonances cannot be addressed with naïve application of traditional bound state electronic structure theory. Non-Hermitian electronic structure methods employing complex basis functions is one way that we may rigorously treat resonances within the framework of traditional electronic structure theory. In this talk, I will discuss our recent work in this area including the methodological extension from single determinant SCF-based approaches to highly correlated levels of wavefunction-based theory such as equation of motion coupled cluster and many-body perturbation theory. These approaches provide a hierarchy of theoretical methods for the computation of positions and widths of molecular resonances. Within this framework, we may also examine properties of resonances including the dependence of these parameters on molecular geometry. Some applications of these methods to temporary anions and dianions will also be discussed.

Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

PubMed

Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

2012-01-01

The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

Copolymers for Drag Reduction in Marie Propulsion: New Molecular Structures with Enhanced Effectiveness

DTIC Science & Technology

1991-05-31

Soluble Polymers: Synthesis, Solution Properties, and Applications, ACS Symposium Series 467, Chapter 22, page 338 (1991). "Molecular- Weight -Distribution...Mississippi 39406-0076 at room temperature to remove low molecular weight polymers and excess KOH. The final products were obtained by freeze-drying...polyelectrolytes due to the presence of the were conducted on a Contraves LS 30 low shear rheometer at a shear long hydrophobic side chains in the polymer

Molecular engineering of fluorescein dyes as complementary absorbers in dye co-sensitized solar cells

DOE PAGES

Pepe, Giulio; Cole, Jacqueline M.; Waddell, Paul G.; ...

2016-09-22

Fluorescein dye derivatives exhibit extended optical absorption up to 500 nm, rendering these compounds suitable as co-absorbers in dye-sensitized solar cells (DSCs). A molecular engineering approach is presented, which embraces this intrinsic optical attribute of fluoresceins, while modifying the dye chemistry to enhance their light harvesting efficiency, in order to effectively tailor them for DSC applications. This approach first realizes relationships between the molecular structure and the optoelectronic properties for a series of five a priori known (parent) fluorescein dyes: 5-carboxyfluorescein (1), a mixture of m-carboxyfluorescein where m = 5 or 6 (2), 5-carboxyfluorescein diacetate (3), 6-carboxyfluorescein diacetate (4), amore » mixture of n-carboxy-2',7'-dichlorofluorescein diacetate where n = 5 or 6 (5). The first step in this approach combines, where available, experimental and computational methods so that electronic structure calculations can also be validated for representative fluorescein dyes. Such calculations can then be used reliably to predict the structure and properties of fluorescein dyes for cases where experimental data are lacking. Structure-function relationships established from this initial step inform the selection of parent dye 1 that is taken forward to the second step in molecular engineering: in silico chemical derivation to re-functionalize 1 for DSC applications. For this purpose, computational calculations are used to extend the charge conjugation in 1 between its donor and acceptor moieties. These structural modifications result in a bathochromic shift of the lowest excitation by ~1.3-1.9 eV (100-170 nm), making the dye optically absorb in the visible region. Further calculations on dye molecules adsorbed onto the surface of a TiO 2 cluster are used to investigate the dye sensitization behavior via dye adsorption energies and anchoring modes. The results of this theoretical investigation lead to two molecularly engineered fluoresceins being proposed to act as co-sensitizers together with a rhodamine dye. This combination of three dyes ensures chemical compatibility, panchromatic absorption, and restores optical absorption dipping otherwise observed in a DSC device at ~350-400 nm owing to the I-/I- 3 electrolyte. Altogether, the results of this study demonstrate that molecular engineering can be used to identify suitable chemical modifications for organic dyes with improved light harvesting properties for photovoltaic applications.« less

Molecular engineering of fluorescein dyes as complementary absorbers in dye co-sensitized solar cells

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

Pepe, Giulio; Cole, Jacqueline M.; Waddell, Paul G.

Fluorescein dye derivatives exhibit extended optical absorption up to 500 nm, rendering these compounds suitable as co-absorbers in dye-sensitized solar cells (DSCs). A molecular engineering approach is presented, which embraces this intrinsic optical attribute of fluoresceins, while modifying the dye chemistry to enhance their light harvesting efficiency, in order to effectively tailor them for DSC applications. This approach first realizes relationships between the molecular structure and the optoelectronic properties for a series of five a priori known (parent) fluorescein dyes: 5-carboxyfluorescein (1), a mixture of m-carboxyfluorescein where m = 5 or 6 (2), 5-carboxyfluorescein diacetate (3), 6-carboxyfluorescein diacetate (4), amore » mixture of n-carboxy-2',7'-dichlorofluorescein diacetate where n = 5 or 6 (5). The first step in this approach combines, where available, experimental and computational methods so that electronic structure calculations can also be validated for representative fluorescein dyes. Such calculations can then be used reliably to predict the structure and properties of fluorescein dyes for cases where experimental data are lacking. Structure-function relationships established from this initial step inform the selection of parent dye 1 that is taken forward to the second step in molecular engineering: in silico chemical derivation to re-functionalize 1 for DSC applications. For this purpose, computational calculations are used to extend the charge conjugation in 1 between its donor and acceptor moieties. These structural modifications result in a bathochromic shift of the lowest excitation by ~1.3-1.9 eV (100-170 nm), making the dye optically absorb in the visible region. Further calculations on dye molecules adsorbed onto the surface of a TiO 2 cluster are used to investigate the dye sensitization behavior via dye adsorption energies and anchoring modes. The results of this theoretical investigation lead to two molecularly engineered fluoresceins being proposed to act as co-sensitizers together with a rhodamine dye. This combination of three dyes ensures chemical compatibility, panchromatic absorption, and restores optical absorption dipping otherwise observed in a DSC device at ~350-400 nm owing to the I-/I- 3 electrolyte. Altogether, the results of this study demonstrate that molecular engineering can be used to identify suitable chemical modifications for organic dyes with improved light harvesting properties for photovoltaic applications.« less

Gene-Transformation-Induced Changes in Chemical Functional Group Features and Molecular Structure Conformation in Alfalfa Plants Co-Expressing Lc-bHLH and C1-MYB Transcriptive Flavanoid Regulatory Genes: Effects of Single-Gene and Two-Gene Insertion.

PubMed

Heendeniya, Ravindra G; Yu, Peiqiang

2017-03-20

Alfalfa ( Medicago sativa L.) genotypes transformed with Lc-bHLH and Lc transcription genes were developed with the intention of stimulating proanthocyanidin synthesis in the aerial parts of the plant. To our knowledge, there are no studies on the effect of single-gene and two-gene transformation on chemical functional groups and molecular structure changes in these plants. The objective of this study was to use advanced molecular spectroscopy with multivariate chemometrics to determine chemical functional group intensity and molecular structure changes in alfalfa plants when co-expressing Lc-bHLH and C1-MYB transcriptive flavanoid regulatory genes in comparison with non-transgenic (NT) and AC Grazeland (ACGL) genotypes. The results showed that compared to NT genotype, the presence of double genes ( Lc and C1 ) increased ratios of both the area and peak height of protein structural Amide I/II and the height ratio of α-helix to β-sheet. In carbohydrate-related spectral analysis, the double gene-transformed alfalfa genotypes exhibited lower peak heights at 1370, 1240, 1153, and 1020 cm -1 compared to the NT genotype. Furthermore, the effect of double gene transformation on carbohydrate molecular structure was clearly revealed in the principal component analysis of the spectra. In conclusion, single or double transformation of Lc and C1 genes resulted in changing functional groups and molecular structure related to proteins and carbohydrates compared to the NT alfalfa genotype. The current study provided molecular structural information on the transgenic alfalfa plants and provided an insight into the impact of transgenes on protein and carbohydrate properties and their molecular structure's changes.

A comparative study of structural and conformational properties of casein kinase-1 isoforms: insights from molecular dynamics and principal component analysis.

PubMed

Singh, Surya Pratap; Gupta, Dwijendra K

2015-04-21

Wnt signaling pathway regulates several developmental processes in human; however recently this pathway has been associated with development of different types of cancers. Casein kinase-1 (CK1) constitutes a family of serine-threonine protein kinase; various members of this family participate in Wnt signal transduction pathway and serve as molecular switch to this pathway. Among the known six isoforms of CK1, in human, at least three isoforms (viz. alpha, delta and epsilon) have been reported as oncogenic. The development of common therapeutics against these kinases is an arduous task; unless we have the detailed information of their tertiary structures and conformational properties. In the present work, the dynamical and conformational properties for each of three isoforms of CK1 are explored through molecular dynamics (MD) simulations. The conformational space distribution of backbone atoms is evaluated using principal component analysis of MD data, which are further validated on the basis of potential energy surface. Based on these analytics, it is suggested that conformational subspace shifts upon binding to ligands and guides the kinase action of CK1 isoforms. Further, this paper as a first effort to concurrently study all the three isoforms of CK1 provides structural basis for development of common anticancer therapeutics against three isoforms of CK1. Copyright © 2015 Elsevier Ltd. All rights reserved.

High-Throughput Characterization of Vapor-Deposited Organic Glasses

NASA Astrophysics Data System (ADS)

Dalal, Shakeel S.

Glasses are non-equilibrium materials which on short timescales behave like solids, and on long timescales betray their liquid-like structure. The most common way of preparing a glass is to cool the liquid faster than it can structurally rearrange. Until recently, most preparation schemes for a glass were considered to result in materials with undifferentiable structure and properties. This thesis utilizes a particular preparation method, physical vapor deposition, in order to prepare glasses of organic molecules with properties otherwise considered to be unobtainable. The glasses are characterized using spectroscopic ellipsometry, both as a dilatometric technique and as a reporter of molecular packing. The results reported here develop ellipsometry as a dilatometric technique on a pair of model glass formers, alpha,alpha,beta-trisnaphthylbenzene and indomethacin. It is found that the molecular orientation, as measured by birefringence, can be tuned by changing the substrate temperature during the deposition. In order to efficiently characterize the properties of vapor-deposited indomethacin as a function of substrate temperature, a high-throughput method is developed to capture the entire interesting range of substrate temperatures in just a few experiments. This high-throughput method is then leveraged to describe molecular mobility in vapor-deposited indomethacin. It is also used to demonstrate that the behavior of organic semiconducting molecules agrees with indomethacin quantitatively, and this agreement has implications for emerging technologies such as light-emitting diodes, photovoltaics and thin-film transistors made from organic molecules.

Molecular dynamics simulations to calculate glass transition temperature and elastic constants of novel polyethers.

PubMed

Sarangapani, Radhakrishnan; Reddy, Sreekantha T; Sikder, Arun K

2015-04-01

Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties. Copyright © 2015 Elsevier Inc. All rights reserved.

Calixarenes in analytical and separation chemistry.

PubMed

Ludwig, R

2000-05-01

Discovered in the 1940's, [1n]metacyclophanes with the common name calix[n]arenes which is derived from for the molecule's shape enjoyed a remarkable interest in almost all fields of chemistry since the 1980's, which is highlighted by several books [1-8]. Over 50 reviews concerning their synthesis, properties and applicabilities were published, many of those with emphasis on organic synthesis and structural properties are cited in [P. 5-6 in 2]. Of interest for analytical chemists are reviews on calixarenes and the structurally related resorcin[n]arenes (or calix[n]resorcarenes) and calixpyrroles concerning potentiometric sensors [9-12], chromo- and fluorophores [13, 14], molecular switches [15], metal ion binding in solution [16-19], redox properties [20] and anion binding [21-24]. Other recent reviews deal with thermodynamic aspects [25], organometallic compounds [26], P-containing calixarenes [27-29], as well as molecular dynamics modeling [30-33]. It is a vital field with over 200 publications per year. Therefore, this article presents only selected results on complexation, solvent extraction and membrane transport with the emphasis on ion and molecular recognition which can be used for analytical purposes, without attempting to cover all available references.

Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

ERIC Educational Resources Information Center

Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

2018-01-01

A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

Determination of Physical and Chemical Structure of New High-Temperature Polymers

DTIC Science & Technology

toward determination of the molecular weight of both perfluorosebacate and perfluoroalkyl ether-linked polymers. In addition, solubility, thermal...thermal properties, and molecular weight. Several samples of the perfluoroalkyl bibenzoxazole polymers were examined. Considerable effort was directed...stability and subambient DTA of the perfluoroalkyl ether- linked polymers (elastomers) were investigated. Samples of the aromatic heterocyclic-ladder type

The Building Blocks of Materials: Gathering Knowledge at the Molecular Level

NASA Technical Reports Server (NTRS)

2003-01-01

Two start-up positions were created within SD46 to pursue developments in the rapidly expanding areas of biomineralization and nano-technology. As envisioned by Dr. Sandor Lehoczy, the new laboratories to be developed must have the capacity to investigate not only processes associated with the self-assembly of molecules but also the examination of self-assembled structures. For these purposes, laboratories capable of performing the intended function, particularly light scattering spectroscopy and atomic force microscopy were created. What follows then are recent advances arising from the development of these new laboratories. With the implementation of the Atomic Force Microscopy Facility, examples of investigations that determine a correlation between the molecular structure of materials and their macroscopic physical properties are provided. In addition, examples of investigations with particular emphasis on the physical properties of protein crystals, at the molecular level, and subsequent macroscopic characteristics are as provided. Finally, progress in fabrication of technology at the nano-scale levels at the developmental stage is also presented.

A DMPA Langmuir monolayer study: from gas to solid phase. An atomistic description by molecular dynamics Simulation.

PubMed

Giner-Casares, J J; Camacho, L; Martín-Romero, M T; Cascales, J J López

2008-03-04

In this work, a DMPA Langmuir monolayer at the air/water interface was studied by molecular dynamics simulations. Thus, an atomistic picture of a Langmuir monolayer was drawn from its expanded gas phase to its final solid condensed one. In this sense, some properties of monolayers that were traditionally poorly or even not reproduced in computer simulations, such as lipid domain formation or pressure-area per lipid isotherm, were properly reproduced in this work. Thus, the physical laws that control the lipid domain formation in the gas phase and the structure of lipid monolayers from the gas to solid condensed phase were studied. Thanks to the atomistic information provided by the molecular dynamics simulations, we were able to add valuable information to the experimental description of these processes and to access experimental data related to the lipid monolayers in their expanded phase, which is difficult or inaccessible to study by experimental techniques. In this sense, properties such as lipids head hydration and lipid structure were studied.

Young's moduli of carbon materials investigated by various classical molecular dynamics schemes

NASA Astrophysics Data System (ADS)

Gayk, Florian; Ehrens, Julian; Heitmann, Tjark; Vorndamme, Patrick; Mrugalla, Andreas; Schnack, Jürgen

2018-05-01

For many applications classical carbon potentials together with classical molecular dynamics are employed to calculate structures and physical properties of such carbon-based materials where quantum mechanical methods fail either due to the excessive size, irregular structure or long-time dynamics. Although such potentials, as for instance implemented in LAMMPS, yield reasonably accurate bond lengths and angles for several carbon materials such as graphene, it is not clear how accurate they are in terms of mechanical properties such as for instance Young's moduli. We performed large-scale classical molecular dynamics investigations of three carbon-based materials using the various potentials implemented in LAMMPS as well as the EDIP potential of Marks. We show how the Young's moduli vary with classical potentials and compare to experimental results. Since classical descriptions of carbon are bound to be approximations it is not astonishing that different realizations yield differing results. One should therefore carefully check for which observables a certain potential is suited. Our aim is to contribute to such a clarification.

The role of the hydrophobic phase in the unique rheological properties of saponin adsorption layers.

PubMed

Golemanov, Konstantin; Tcholakova, Slavka; Denkov, Nikolai; Pelan, Eddie; Stoyanov, Simeon D

2014-09-28

Saponins are a diverse class of natural, plant derived surfactants, with peculiar molecular structure consisting of a hydrophobic scaffold and one or several hydrophilic oligosaccharide chains. Saponins have strong surface activity and are used as natural emulsifiers and foaming agents in food and beverage, pharmaceutical, ore processing, and other industries. Many saponins form adsorption layers at the air-water interface with extremely high surface elasticity and viscosity. The molecular origin of the observed unique interfacial visco-elasticity of saponin adsorption layers is of great interest from both scientific and application viewpoints. In the current study we demonstrate that the hydrophobic phase in contact with water has a very strong effect on the interfacial properties of saponins and that the interfacial elasticity and viscosity of the saponin adsorption layers decrease in the order: air > hexadecane ≫ tricaprylin. The molecular mechanisms behind these trends are analyzed and discussed in the context of the general structure of the surfactant adsorption layers at various nonpolar phase-water interfaces.

Effect of chemical substitutions on photo-switching properties of 3-hydroxy-picolinic acid studied by ab initio methods

NASA Astrophysics Data System (ADS)

Rode, Michał F.; Sobolewski, Andrzej L.

2014-02-01

Effect of chemical substitutions to the molecular structure of 3-hydroxy-picolinic acid on photo-switching properties of the system operating on excited-state intramolecular double proton transfer (d-ESIPT) process [M. F. Rode and A. L. Sobolewski, Chem. Phys. 409, 41 (2012)] was studied with the aid of electronic structure theory methods. It was shown that simultaneous application of electron-donating and electron-withdrawing substitutions at certain positions of the molecular frame increases the height of the S0-state tautomerization barrier (ensuring thermal stability of isomers) and facilitates a barrierless access to the S1/S0 conical intersection from the Franck-Condon region of the S1 potential-energy surface. Results of study point to the conclusion that the most challenging issue for practical design of a fast molecular photoswitch based on d-ESIPT phenomenon are to ensure a selectivity of optical excitation of a given tautomeric form of the system.

Field determination and QSPR prediction of equilibrium-status soil/vegetation partition coefficient of PCDD/Fs.

PubMed

Li, Li; Wang, Qiang; Qiu, Xinghua; Dong, Yian; Jia, Shenglan; Hu, Jianxin

2014-07-15

Characterizing pseudo equilibrium-status soil/vegetation partition coefficient KSV, the quotient of respective concentrations in soil and vegetation of a certain substance at remote background areas, is essential in ecological risk assessment, however few previous attempts have been made for field determination and developing validated and reproducible structure-based estimates. In this study, KSV was calculated based on measurements of seventeen 2,3,7,8-substituted PCDD/F congeners in soil and moss (Dicranum angustum), and rouzi grass (Thylacospermum caespitosum) of two background sites, Ny-Ålesund of the Arctic and Zhangmu-Nyalam region of the Tibet Plateau, respectively. By both fugacity modeling and stepwise regression of field data, the air-water partition coefficient (KAW) and aqueous solubility (SW) were identified as the influential physicochemical properties. Furthermore, validated quantitative structure-property relationship (QSPR) model was developed to extrapolate the KSV prediction to all 210 PCDD/F congeners. Molecular polarizability, molecular size and molecular energy demonstrated leading effects on KSV. Copyright © 2014 Elsevier B.V. All rights reserved.

Biomineralization-inspired synthesis of functional organic/inorganic hybrid materials: organic molecular control of self-organization of hybrids.

PubMed

Arakaki, Atsushi; Shimizu, Katsuhiko; Oda, Mayumi; Sakamoto, Takeshi; Nishimura, Tatsuya; Kato, Takashi

2015-01-28

Organisms produce various organic/inorganic hybrid materials, which are called biominerals. They form through the self-organization of organic molecules and inorganic elements under ambient conditions. Biominerals often have highly organized and hierarchical structures from nanometer to macroscopic length scales, resulting in their remarkable physical and chemical properties that cannot be obtained by simple accumulation of their organic and inorganic constituents. These observations motivate us to create novel functional materials exhibiting properties superior to conventional materials--both synthetic and natural. Herein, we introduce recent progress in understanding biomineralization processes at the molecular level and the development of organic/inorganic hybrid materials by these processes. We specifically outline fundamental molecular studies on silica, iron oxide, and calcium carbonate biomineralization and describe material synthesis based on these mechanisms. These approaches allow us to design a variety of advanced hybrid materials with desired morphologies, sizes, compositions, and structures through environmentally friendly synthetic routes using functions of organic molecules.

Interface electronic structures of reversible double-docking self-assembled monolayers on an Au(111) surface

PubMed Central

Zhang, Tian; Ma, Zhongyun; Wang, Linjun; Xi, Jinyang; Shuai, Zhigang

2014-01-01

Double-docking self-assembled monolayers (DDSAMs), namely self-assembled monolayers (SAMs) formed by molecules possessing two docking groups, provide great flexibility to tune the work function of metal electrodes and the tunnelling barrier between metal electrodes and the SAMs, and thus offer promising applications in both organic and molecular electronics. Based on the dispersion-corrected density functional theory (DFT) in comparison with conventional DFT, we carry out a systematic investigation on the dual configurations of a series of DDSAMs on an Au(111) surface. Through analysing the interface electronic structures, we obtain the relationship between single molecular properties and the SAM-induced work-function modification as well as the level alignment between the metal Fermi level and molecular frontier states. The two possible conformations of one type of DDSAM on a metal surface reveal a strong difference in the work-function modification and the electron/hole tunnelling barriers. Fermi-level pinning is found to be a key factor to understand the interface electronic properties. PMID:24615153

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

PubMed Central

Grigorenko, B.L.; Savitsky, A.P.

2009-01-01

Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical-molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers. PMID:22649601

Physical properties of organic fullerene cocrystals

NASA Astrophysics Data System (ADS)

Macovez, Roberto

2017-12-01

The basic facts and fundamental properties of binary fullerene cocrystals are reviewed, focusing especially on solvates and salts of Buckminsterfullerene (C60), and hydrates of hydrophilic C60 derivatives. The examined properties include the lattice structure and the presence of orientational disorder and/or rotational dynamics (of both fullerenes and cocrystallizing moieties), thermodynamic properties such as decomposition enthalpies, and charge transport properties. Both thermodynamic properties and molecular orientational disorder shed light on the extent of intermolecular interactions in these binary solid-state systems. Comparison is carried out also with pristine fullerite and with the solid phases of functionalized C60. Interesting experimental findings on binary fullerene cocrystals include the simultaneous occurrence of rotations of both constituent molecular species, crystal morphologies reminiscent of quasi-crystalline behaviour, the observation of proton conduction in hydrate solids of hydrophilic fullerene derivatives, and the production of super-hard carbon materials by application of high pressures on solvated fullerene crystals.

Sequence-structure correlations in silk: Poly-Ala repeat of N. clavipes MaSp1 is naturally optimized at a critical length scale.

PubMed

Bratzel, Graham; Buehler, Markus J

2012-03-01

Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly β-sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of 3(10)-helix type structures and β-turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined β-sheet nanocrystals. For poly-alanine lengths below six, the β-sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the β-sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Molecular structures of (3-aminopropyl)trialkoxysilane on hydroxylated barium titanate nanoparticle surfaces induced by different solvents and their effect on electrical properties of barium titanate based polymer nanocomposites

NASA Astrophysics Data System (ADS)

Fan, Yanyan; Wang, Guanyao; Huang, Xingyi; Bu, Jing; Sun, Xiaojin; Jiang, Pingkai

2016-02-01

Surface modification of nanoparticles by grafting silane coupling agents has proven to be a significant approach to improve the interfacial compatibility between inorganic filler and polymer matrix. However, the impact of grafted silane molecular structure after the nanoparticle surface modification, induced by the utilized solvents and the silane alkoxy groups, on the electrical properties of the corresponding nanocomposites, has been seldom investigated. Herein, the silanization on the surface of hydroxylated barium titanate (BT-OH) nanoparticles was introduced by using two kinds of trialkoxysilane, 3-aminopropyltriethoxysilane (AMEO) and 3-aminopropyltrimethoxysilane (AMMO), with different solvents (toluene and ethanol), respectively. Solid-state 13C, 29Si nuclear magnetic resonance (NMR) spectroscopy and high-resolution X-ray photoelectron spectroscopy (XPS) were employed to validate the structure differences of alkoxysilane attachment to the nanoparticles. The effect of alkoxysilane structure attached to the nanoparticle surface on the dielectric properties of the BT based poly(vinylidene fluoride) (PVDF) nanocomposites were investigated. The results reveal that the solvents used for BT nanoparticle surface modification exhibit a significant effect on the breakdown strength of the nanocomposites. Nevertheless, the alkoxy groups of silane show a marginal influence on the dielectric properties of the nanocomposites. These research results provide important insights into the fabrication of advanced polymer nanocomposites for dielectric applications.

Effect of different types of surfactants on the microstructure of methyltrimethoxysilane-derived silica aerogels: A combined experimental and computational approach.

PubMed

Vareda, João P; Maximiano, Pedro; Cunha, Luís P; Ferreira, André F; Simões, Pedro N; Durães, Luísa

2018-02-15

Surfactants interfere with sol-gel particle/pore growth, influencing the structure and properties of silica aerogels. Their ability to induce microscopic changes in the aerogel's structure may be useful to improve/control the thermal insulation performance of aerogels. The influence of different types of surfactants (anionic, cationic and non-ionic) on the microstructural arrangement and macroscopic properties of methyltrimethoxysilane (MTMS)-based aerogels was evaluated for the first time, using an experimental and computational comparative approach. Molecular dynamics simulations were performed based on two representative silica molecular structures derived from MTMS, while the experimentally-obtained silica aerogels were characterized in terms of chemical/structural/mechanical/thermal insulation properties. The use of both hexadecyltrimethylammonium bromide (CTAB) and sodium dodecylsulfate (SDS) led to a decrease in bulk density, thermal conductivity and average pore size of the aerogels, with notorious increase of their flexibility. The observed changes were due to microstructural arrangements, as evidenced by scanning electron microscopy (SEM). However, the non-ionic surfactant, Pluronic F-127, did not have a positive impact on the desired properties. Globally, the simulation results support the experimental findings, suggesting differentiated microstructural changes induced by the use of cationic or anionic surfactants. The addition of CTAB and SDS generally resulted in smaller or larger silica aggregates, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

Ligand structure and mechanical properties of single-nanoparticle thick membranes

DOE PAGES

Salerno, Kenneth Michael; Bolintineanu, Dan S.; Lane, J. Matthew D.; ...

2015-06-16

We believe that the high mechanical stiffness of single-nanoparticle-thick membranes is the result of the local structure of ligand coatings that mediate interactions between nanoparticles. These ligand structures are not directly observable experimentally. We use molecular dynamics simulations to observe variations in ligand structure and simultaneously measure variations in membrane mechanical properties. We have shown previously that ligand end group has a large impact on ligand structure and membrane mechanical properties. Here we introduce and apply quantitative molecular structure measures to these membranes and extend analysis to multiple nanoparticle core sizes and ligand lengths. Simulations of nanoparticle membranes with amore » nanoparticle core diameter of 4 or 6 nm, a ligand length of 11 or 17 methylenes, and either carboxyl (COOH) or methyl (CH 3) ligand end groups are presented. In carboxyl-terminated ligand systems, structure and interactions are dominated by an end-to-end orientation of ligands. In methyl-terminated ligand systems large ordered ligand structures form, but nanoparticle interactions are dominated by disordered, partially interdigitated ligands. Core size and ligand length also affect both ligand arrangement within the membrane and the membrane's macroscopic mechanical response, but are secondary to the role of the ligand end group. Additionally, the particular end group (COOH or CH 3) alters the nature of how ligand length, in turn, affects the membrane properties. The effect of core size does not depend on the ligand end group, with larger cores always leading to stiffer membranes. Asymmetry in the stress and ligand density is observed in membranes during preparation at a water-vapor interface, with the stress asymmetry persisting in all membranes after drying.« less