Search results for: molecular and supramolecular structure

Authors: Y. Megrous, A. Chouaih, F. Hamzaoui

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The crystal structure of 4-Methyl-7-(salicylideneamino)coumarin C17H13NO3has been determined using X-ray diffraction to establish the configuration and stereochemistry of the molecule. This crystal is characterized by its nolinear activity. The molecular electron charge density distribution of the title compound is described accurately using the multipolar model of Hansen and Coppens. The net atomic charge and the molecular dipole moment in-crystal have been determined in order to understand the nature of inter-and intramolecular charge transfer. The study present the thermal motion and the structural analysis obtained from the least-square refinement on F2,this study has also allowed us to determine the electrostatic potential and therefore locate the electropositive part and the electronegative part in molecular scale of the title compound.

Keywords: electron charge density, net atomic charge, molecular dipole moment, X-ray diffraction

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Authors: Tsu-Hsu Yen

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The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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Authors: Zohreh Derikvand, Hadis Cheraghi, Azadeh Azadbakht, Vaclav Eigner, Michal Dusek

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Two new one and two dimensional metal organic coordination polymers of Cu(II), [Cu(3-nph)2(H2O)2pz]n (1) and Ag(I), {[Ag(3-nph)pz].H2O}n (2) with pyrazine (pz) and 3- nitrophthalic acid (3-nph) have been synthesized and characterized by elemental analysis, spectral (IR, UV-Vis), thermal (TG/DTG) analysis and single crystal X-ray diffraction. We used these compounds to preparation modified electrode with Au/Pt nanosparticles in order to investigation electrochemistry and electrocatalysis activities. The surface structure and composition of the sensor were characterized by scanning electron microscopy (SEM). The Ag(I) coordination polymer shows a 2D layer structure constructed from dinuclear silver (I) building blocks in which two crystallographically Ag+ ions are connected to each other by a covalent bond. The pyrazine ligands adopt μ2 bridging modes, linking the metal centers into a one and two -dimensional coordination framework in 1 and 2. The two AgI cations are surrounded by pyrazine and 3-nitrophthalate mono anions and indicate distorted tetrahedral geometry. In the crystal structures of Ag(I) complex there are non-classical hydrogen bonding arrangements, C–O•••π and π–π stacking interactions. In Cu(II) coordination polymer, the coordination geometry around Cu(II) atom is a distorted octahedron. Interestingly, the structural analysis illustrates that the strong and weak hydrogen bond accompanied with C–H•••π and C–O•••π stacking interactions assemble the crystal structure of 1 and 2 into fascinating 3D supramolecular architecture.

Keywords: 3-nithrophethalic acid, crystal structure, coordination polymer, electrocatalysis

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Authors: Van Tran Thi Thuy, Dukjoon Kim

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A series of pH- and thermosensitive poly(N-isopropyl acrylamide-co-acrylic acid) were synthesized by radical polymerization and grafted on poly succinimide backbones. The poly succinimide derivatives synthesized were coated on iron oxide magnetic nanoparticles for potential applications in drug delivery systems with theranostic and molecular imaging. The structure of polymer shell was confirmed by FT-IR, H-NMR spectroscopies. Its thermal behavior was tested by UV-Vis spectroscopy. The particle size and its distribution are measured by dynamic light scattering (DLS) and transmission electron microscope (TEM). The mean diameter of the core-shell structure is from 20 to 80 nm.

Keywords: magnetic, nano, PNIPAM, polysuccinimide

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Authors: Archana Gupta, Rajesh Kumar

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The chemistry of chalcones has generated intensive scientific studies throughout the world. Especially, interest has been focused on the synthesis and biodynamic activities of chalcones. The blue light transmittance, excellent crystallizability and the two planar rings connected through a conjugated double bond show that chalcone derivatives are superior nonlinear organic compounds. 3-(2-Chloro-6-fluoro¬phen¬yl)-1-(2-thien¬yl) prop-2-en-1-one, 3-(2, 4- Dichlorophenyl) – 1 - (4-methylphenyl) – prop -2-en-1-one, (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one are some chalcone derivatives exhibiting non linear optical (NLO) properties. NLO materials have been extensively investigated in recent years as they are the key elements for photonic technologies of optical communication, optical interconnect oscillator, amplifier, frequency converter etc. Due to their high molecular hyperpolarizabilities, organic materials display a number of significant NLO properties. Experimental measurements and theoretical calculations on molecular hyperpolarizability β have become one of the key factors in the design of second order NLO materials. Theoretical determination of hyperpolarizability is quite useful both in understanding the relationship between the molecular structure and NLO properties. It also provides a guideline to experimentalists for the design and synthesis of organic NLO materials. Quantum-chemical calculations have made an important contribution to the understanding of the electronic polarization underlying the molecular NLO processes and the establishment of structure–property relationships. In the present investigation, the detailed vibrational analysis of some chalcone derivatives is taken up to understand the correlation of the charge transfer interaction and the NLO activity of the molecules based on density functional theory calculations. The vibrational modes contributing toward the NLO activity have been identified and analyzed. Rather large hyperpolarizability derived by theoretical calculations suggests the possible future use of these compounds for non-linear optical applications. The study suggests the importance of π - conjugated systems for non-linear optical properties and the possibility of charge transfer interactions. We hope that the results of the present study of chalcone derivatives are of assistance in development of new efficient materials for technological applications.

Keywords: hyperpolarizability, molecular structure, NLO material, quantum chemical calculations

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Authors: Amanda M. Tadini, Houssam Hajjoul, Gustavo Nicolodelli, Stéphane Mounier, Célia R. Montes, Débora M. B. P. Milori

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Soil organic matter (SOM) plays an important role in maintaining soil productivity and accounting for the promotion of biological diversity. The main components of the SOM are the humic substances which can be fractionated according to its solubility in humic acid (HA), fulvic acids (FA) and humin (HU). The determination of the chemical properties of organic matter as well as its interaction with metallic species is an important tool for understanding the structure of the humic fractions. Fluorescence spectroscopy has been studied as a source of information about what is happening at the molecular level in these compounds. Specially, soils of Amazon region are an important ecosystem of the planet. The aim of this study is to understand the molecular and structural composition of HA samples from Spodosol of Amazonia using the fluorescence Emission-Excitation Matrix (EEM) and Time Resolved Fluorescence Spectroscopy (TRFS). The results showed that the samples of HA showed two fluorescent components; one has a more complex structure and the other one has a simpler structure, which was also seen in TRFS through the evaluation of each sample lifetime. Thus, studies of this nature become important because it aims to evaluate the molecular and structural characteristics of the humic fractions in the region that is considered as one of the most important regions in the world, the Amazon.

Keywords: Amazonian soil, characterization, fluorescence, humic acid, lifetime

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

Abstract:

The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G(d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G(d,p) method show good agreement with experimental X-ray data. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide, polarizability

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Authors: Fatimah Zawani Abdullah, Shereena Mohd Arif, Nurul Malim

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The study of molecular similarity search in chemical database is increasingly widespread, especially in the area of drug discovery. Similarity search is an application in the field of Chemoinformatics to measure the similarity between the molecular structure which is known as the query and the structure of chemical compounds in the database. Similarity search is also one of the approaches in virtual screening which involves computational techniques and scoring the probabilities of activity. The main objective of this work is to determine the best fingerprint when compared to the other five fingerprints selected in this study using PubChem chemical dataset. This paper will discuss the similarity searching process conducted using 6 types of descriptors, which are ECFP4, ECFC4, FCFP4, FCFC4, SRECFC4 and SRFCFC4 on 15 activity classes of PubChem dataset using Tanimoto coefficient to calculate the similarity between the query structures and each of the database structure. The results suggest that ECFP4 performs the best to be used with Tanimoto coefficient in the PubChem dataset.

Keywords: 2D fingerprints, Tanimoto, PubChem, similarity searching, chemoinformatics

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Authors: Alya Harichane, Abderraouf Achour, Abdelbaki Benmounah

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The main difficulty encountered in the formulation of high-performance concrete (HPC) consists in choosing the most efficient cement-superplasticizer pair allowing to obtain maximum water reduction, good workability of the concrete in the fresh state, and very good mechanical resistance in the hardened state. The aim of this work is to test the efficiency of three polycarboxylate ether-based superplasticizers (PCE) marketed in Algeria with CEMI 52.5 R cement and to study the effect of chemical structure of PCE on zeta potential, rheological and mechanical properties of cement pastes. The property of the polymers in cement was tested by a Malvern Zetasizer 2000 apparatus and VT 550 viscometer. Results showed that the zeta potential and its rheological properties are related to the molecular weight and the density carboxylic of PCE. The PCE with a moderate molecular weight and the highest carboxylic groups had the best dispersion (high value of zeta potential) and lowest viscosity. The effect of the chemical structure of PCEs on mechanical properties is evaluated by the formulation of cement mortar with these PCEs. The result shows that there is a correlation between the zeta potential of polymer and the compressive strength of cement paste.

Keywords: molecular weight, polycarboxylate-ether superplasticizer, rheology, zeta potential

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Authors: Salem El-Tohami Ashoor

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Here we show that the reduction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, this was optimization by using density functional theory (DFT) and then was comparing with experimental data, also other possibility of Cp interacted with ion metal were tested like η1 ,η2 ,η3 and η4 under optimization system. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP ( Becke)( Lee–Yang–Parr ) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of chromium cyclopentadienyl. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Chromium(III) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Raimoana Frogier, Luc Girard, Pierre Bauduin, Diane Rebiscoul, Olivier Diat

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Nano-ions (NIs) are ionic species or clusters of nanometric size. Their low charge density and the delocalization of their charges give special properties to some of NIs belonging to chemical classes of polyoxometalates (POMs) or boron clusters. They have the particularity of interacting non-covalently with neutral hydrated surface or interfaces such as assemblies of surface-active molecules (micelles, vesicles, lyotropic liquid crystals), foam bubbles or emulsion droplets. This makes possible to classify those NIs in the Hofmeister series as superchaotropic ions. The mechanism of adsorption is complex, linked to the simultaneous dehydration of the ion and the molecule or supramolecular assembly with which it can interact, all with an enthalpic gain on the free energy of the system. This interaction process is reversible and is sufficiently pronounced to induce changes in molecular and supramolecular shape or conformation, phase transitions in the liquid phase, all at sub-millimolar ionic concentrations. This new property of some NIs opens up new possibilities for applications in fields as varied as biochemistry for solubilization, recovery of metals of interest by foams in the form of NIs... In order to better understand the physico-chemical mechanisms at the origin of this interaction, we use silicon wafers functionalized by non-ionic oligomers (polyethylene glycol chains or PEG) to study in situ by X-ray reflectivity this interaction of NIs with the grafted chains. This study carried out at ESRF (European Synchrotron Radiation Facility) and has shown that the adsorption of the NIs, such as POMs, has a very fast kinetics. Moreover the distribution of the NIs in the grafted PEG chain layer was quantify. These results are very encouraging and confirm what has been observed on soft interfaces such as micelles or foams. The possibility to play on the density, length and chemical nature of the grafted chains makes this system an ideal tool to provide kinetic and thermodynamic information to decipher the complex mechanisms at the origin of this adsorption.

Keywords: adsorption, nano-ions, solid-liquid interface, superchaotropicity

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Authors: Nataša Kalajdžija, Strahinja Kovačević, Davor Lončar, Sanja Podunavac Kuzmanović, Lidija Jevrić

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In order to investigate the relationship between retention and structure, a quantitative Structure Retention Relationships (QSRRs) study was applied for the prediction of retention times of a set of 23 secoestrane derivatives in a reversed-phase thin-layer chromatography. After the calculation of molecular descriptors, a suitable set of molecular descriptors was selected by using step-wise multiple linear regressions. Artificial Neural Network (ANN) method was employed to model the nonlinear structure-activity relationships. The ANN technique resulted in 5-6-1 ANN model with the correlation coefficient of 0.98. We found that the following descriptors: Critical pressure, total energy, protease inhibition, distribution coefficient (LogD) and parameter of lipophilicity (miLogP) have a significant effect on the retention times. The prediction results are in very good agreement with the experimental ones. This approach provided a new and effective method for predicting the chromatographic retention index for the secoestrane derivatives investigated.

Keywords: lipophilicity, QSRR, RP TLC retention, secoestranes

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Authors: Jayanthi Sivaraman

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Claudins are the important components of the tight junctions that play a key role in paracellular permeability. Among various members of Claudin family, Claudin 4 (CLDN4) is found to be overexpressed in ovarian, pancreatic carcinomas and other epithelial malignancies. Therefore, in this study, an attempt has been made to identify potent inhibitors for CLDN4 from the ZINC database using virtual screening, molecular docking and molecular dynamics simulations. A well refined molecular model of CLDN4 was built using Prime of Schrodinger v10.2(Template- PDB ID: 4P79). Approximately, 6 million compounds from ZINC database are subjected to high-throughput virtual screening (HTVS) against the active site of CLDN4. Molecular docking using GLIDE predicted ARG31, ASN142, ASP146 and ARG158 as critically important residues. Furthermore, three compounds from ZINC database (ZINC96331839, ZINC36533519 and ZINC75819394) showed highly promising ADME properties and binding affinity with stable conformation. The therapeutic efficiency of these lead compounds is evaluated and confirmed by in-vitro and in-vivo studies which leads to the development of novel anti-cancer drugs.

Keywords: ADME property, inhibitors, molecular docking, virtual screening

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Authors: Jeoungsu Na, Jaehawn Lee, Changil Hong, Suhee Kim

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A molecular dynamics simulation in a converging-diverging nozzle was performed to study molecular collisions and their influence to average flow velocity according to a variety of vacuum levels. The static pressures and the dynamic pressure exerted by the molecule collision on the selected walls were compared to figure out the intensity variances of the directional flows. With pressure differences constant between the entrance and the exit of the nozzle, the numerical experiment was performed for molecular velocities and directional flows. The result shows that the velocities increased at the nozzle exit as the vacuum level gets higher in that area because less molecular collisions.

Keywords: cavitation, molecular collision, nozzle, vacuum, velocity increase

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Authors: Abhishek Kumar Gupta

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Atomistic Molecular Dynamics (MD) Simulations have been performed to study the effect of monovalent salt i.e. NaCl concentration (Cs) and chain degree of neutralization (f) on the structure and dynamics of anionic poly(methacrylic acid) (PMA) in dilute aqueous solutions. In the present study, the attention is to unveil the conformational structure, hydrogen-bonding, local polyion-counterion structure, h-bond dynamics, chain dynamics and thermodynamic enthalpy of solvation of a-PMA in dilute aqueous solutions as a function of salt concentration, Cs and f. The results have revealed that at low salt concentration, the conformational radius of gyration (Rg) increases and then decreases reaching a maximum in agreement with the reported light scattering experimental results. The Rg at f = 1 shows a continual decrease and acquire a plateau value at higher salt concentration in agreement with results obtained by light scattering experiments. The radial distribution functions between PMA, salt and water atoms has been computed with respect to atom and centre-of-mass to understand the intermolecular structure in detail. The results pertaining to PMA chain conformations and hydrogen bond autocorrelation function showcasing the h-bond dynamics will be presented. The results pertaining to chain dynamics will be presented. The results pertaining to counterion condensation on the PMA chain shows greater condensation of Na+ ions on to the carboxylate ions with increase in salt concentration. Moreover, the solvation enthalpy of the system as a function of salt concentration will be presented.

Keywords: conformations, molecular dynamics simulations, NaCl concentration, radial distribution functions

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Authors: S. Paszkiewicz, A. Zubkiewicz, A. Szymczyk, D. Pawlikowska, I. Irska, E. Piesowicz, A. Linares, T. A. Ezquerra

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Over the last century, the world has become increasingly dependent on oil as its main source of chemicals and energy. Driven largely by the strong economic growth of India and China, demand for oil is expected to increase significantly in the coming years. This growth in demand, combined with diminishing reserves, will require the development of new, sustainable sources for fuels and bulk chemicals. Biomass is an attractive alternative feedstock, as it is widely available carbon source apart from oil and coal. Nowadays, academic and industrial research in the field of polymer materials is strongly oriented towards bio-based alternatives to petroleum-derived plastics with enhanced properties for advanced applications. In this context, 2,5-furandicarboxylic acid (FDCA), a biomass-based chemical product derived from lignocellulose, is one of the most high-potential biobased building blocks for polymers and the first candidate to replace the petro-derived terephthalic acid. FDCA has been identified as one of the top 12 chemicals in the future, which may be used as a platform chemical for the synthesis of biomass-based polyester. The aim of this study is to synthesize and characterize the multiblock copolymers containing rigid segments of poly(trimethylene 2,5-furanoate) (PTF) and soft segments of poly(tetramethylene oxide) (PTMO) with excellent elastic properties or aliphatic polyesters of polycaprolactone (PCL). Two series of PTF based copolymers, i.e., PTF-block-PTMO-T and PTF-block-PCL-T, with different content of flexible segments were synthesized by means of a two-step melt polycondensation process and characterized by various methods. The rigid segments of PTF, as well as the flexible PTMO/or PCL ones, were randomly distributed along the chain. On the basis of 1H NMR, SAXS and WAXS, DSC an DMTA results, one can conclude that both phases were thermodynamically immiscible and the values of phase transition temperatures varied with the composition of the copolymer. The copolymers containing 25, 35 and 45wt.% of flexible segments (PTMO) exhibited elastomeric property characteristics. Moreover, with respect to the flexible segments content, the temperatures corresponding to 5%, 25%, 50% and 90% mass loss as well as the values of tensile modulus decrease with the increasing content of aliphatic polyether or aliphatic polyester in the composition.

Keywords: furan based polymers, multiblock copolymers, supramolecular structure, functional properties

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Authors: Sonam Chorol, Sharvan Kumar, Pritam Mukhopadhyay

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In biology, supramolecular systems require the use of chemical fuels to stay in sustained nonequilibrium steady states termed dissipative self-assembly in contrast to synthetic self-assembly. Biomimicking these natural dynamic systems, some studies have demonstrated artificial self-assembly under nonequilibrium utilizing various forms of energies (fuel) such as chemical, redox, and pH. Naphthalene diimides (NDIs) are well-known organic molecules in supramolecular architectures with high electron affinity and have applications in controlled electron transfer (ET) reactions, etc. Herein, we report the endergonic ET from tetraphenylborate to highly electron-deficient phosphonium NDI²+ dication to generate NDI•+ radical. The formation of radicals was confirmed by UV-Vis-NIR absorption spectroscopy. Electron-donor and electron-acceptor energy levels were calculated from experimental electrochemistry and theoretical DFT analysis. The HOMO of the electron donor locates below the LUMO of the electro-acceptor. This indicates that electron transfer is endergonic (ΔE°ET = negative). The endergonic ET from NaBPh₄ to NDI²+ dication was achieved thermodynamically by the formation of coupled biphenyl product confirmed by GC-MS analysis. NDI molecule bearing octyl phosphonium at the core and H-bond forming imide moieties at the axial position forms a gel. The rheological properties of purified radical ion NDI⦁+ gels were evaluated. The atomic force microscopy studies reveal the formation of large branching-type networks with a maximum height of 70-80 nm. The endergonic ET from NaBPh₄ to NDI²+ dication was used to design the assembly and disassembly redox reaction cycle using reducing (NaBPh₄) and oxidizing agents (Br₂) as chemical fuels. A part of NaBPh₄ is used to drive assembly, while a fraction of the NaBPh₄ is dissipated by forming a useful product. The system goes back to the disassembled NDI²+ dication state with the addition of Br₂. We think bioinspired dissipative self-assembly is the best approach to developing future lifelike materials with autonomous behavior.

Keywords: Ionic-gel, redox-cycle, self-assembly, useful product

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Authors: Serkan Sayin, Songul F. Varol

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High attention on the organic light-emitting diodes has been paid since their efficient properties in the flat panel displays, and solid-state lighting was realized. Because of their high efficient electroluminescence, brightness and providing eminent in the emission range, organic light emitting diodes have been preferred a material compared with the other materials consisting of the liquid crystal. Calixarenes obtained from the reaction of p-tert-butyl phenol and formaldehyde in a suitable base have been potentially used in various research area such as catalysis, enzyme immobilization, and applications, ion carrier, sensors, nanoscience, etc. In addition, their tremendous frameworks, as well as their easily functionalization, make them an effective candidate in the applied chemistry. Herein, a calix[4]arene derivative has been synthesized, and its structure has been fully characterized using Fourier Transform Infrared Spectrophotometer (FTIR), proton nuclear magnetic resonance (¹H-NMR), carbon-13 nuclear magnetic resonance (¹³C-NMR), liquid chromatography-mass spectrometry (LC-MS), and elemental analysis techniques. The calixarene derivative has been employed as an emitting layer in the fabrication of the organic light-emitting diodes. The optical and electrochemical features of calixarane-contained organic light-emitting diodes (Clx-OLED) have been also performed. The results showed that Clx-OLED exhibited blue emission and high external quantum efficacy. As a conclusion obtained results attributed that the synthesized calixarane derivative is a promising chromophore with efficient fluorescent quantum yield that provides it an attractive candidate for fabricating effective materials for fluorescent probes and labeling studies. This study was financially supported by the Scientific and Technological Research Council of Turkey (TUBITAK Grant no. 117Z402).

Keywords: calixarene, OLED, supramolecular chemistry, synthesis

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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Authors: Ling Dai

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Surface-sensing devices such as atomic force microscope have been widely used to characterize the surface structure and properties of nanoscale polymer films. However, using molecular dynamics simulations, we show that there is intrinsic and unavoidable inelastic deformation at polymer surfaces induced by the sensing tip. For linear chain polymers like perfluoropolyether, such tip-induced deformation derives from the differences in the atomic interactions which are atomic specie-based Van der Waals interactions, and resulting in atomic shuffling and causing inelastic alternation in both molecular structures and mechanical properties at the regions of the polymer surface. For those aromatic chain polymers like epoxy, the intrinsic deformation is depicted as the intra-chain rotation of aromatic rings and kinking of linear atomic connections. The present work highlights the need to reinterpret the data obtained from surface-sensing tests by considering this intrinsic inelastic deformation occurring at polymer surfaces.

Keywords: polymer, surface, nano, molecular dynamics

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Authors: Lidija R. Jevrić, Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević

Abstract:

Quantitative structure-retention relationship (QSRR) analysis was used to predict the chromatographic behavior of s-triazine derivatives by using theoretical descriptors computed from the chemical structure. Fundamental basis of the reported investigation is to relate molecular topological descriptors with chromatographic behavior of s-triazine derivatives obtained by reversed-phase (RP) thin layer chromatography (TLC) on silica gel impregnated with paraffin oil and applied ethanol-water (φ = 0.5-0.8; v/v). Retention parameter (RM0) of 14 investigated s-triazine derivatives was used as dependent variable while simple connectivity index different orders were used as independent variables. The best QSRR model for predicting RM0 value was obtained with simple third order connectivity index (3χ) in the second-degree polynomial equation. Numerical values of the correlation coefficient (r=0.915), Fisher's value (F=28.34) and root mean square error (RMSE = 0.36) indicate that model is statistically significant. In order to test the predictive power of the QSRR model leave-one-out cross-validation technique has been applied. The parameters of the internal cross-validation analysis (r2CV=0.79, r2adj=0.81, PRESS=1.89) reflect the high predictive ability of the generated model and it confirms that can be used to predict RM0 value. Multivariate classification technique, hierarchical cluster analysis (HCA), has been applied in order to group molecules according to their molecular connectivity indices. HCA is a descriptive statistical method and it is the most frequently used for important area of data processing such is classification. The HCA performed on simple molecular connectivity indices obtained from the 2D structure of investigated s-triazine compounds resulted in two main clusters in which compounds molecules were grouped according to the number of atoms in the molecule. This is in agreement with the fact that these descriptors were calculated on the basis of the number of atoms in the molecule of the investigated s-triazine derivatives.

Keywords: s-triazines, QSRR, chemometrics, chromatography, molecular descriptors

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Authors: Strahinja Kovačević, Sanja Podunavac-Kuzmanović, Lidija Jevrić, Milica Karadžić

Abstract:

The present study is based on the quantitative structure-activity relationship (QSAR) analysis of eighteen compounds with anti-prion activity. The structures and anti-prion activities (expressed in response units, RU%) of the analyzed compounds are taken from CHEMBL database. In the first step of analysis 85 molecular descriptors were calculated and based on them the hierarchical cluster analysis (HCA) and principal component analysis (PCA) were carried out in order to detect potential significant similarities or dissimilarities among the studied compounds. The calculated molecular descriptors were physicochemical, lipophilicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) descriptors. The first stage of the QSAR analysis was simple linear regression modeling. It resulted in one acceptable model that correlates Henry's law constant with RU% units. The obtained 2D-QSAR model was validated by cross-validation as an internal validation method. The validation procedure confirmed the model’s quality and therefore it can be used for prediction of anti-prion activity. The next stage of the analysis of anti-prion activity will include 3D-QSAR and molecular docking approaches in order to select the most promising compounds in treatment of prion diseases. These results are the part of the project No. 114-451-268/2016-02 financially supported by the Provincial Secretariat for Science and Technological Development of AP Vojvodina.

Keywords: anti-prion activity, chemometrics, molecular modeling, QSAR

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Authors: Nikhil Agrawal, Adam A. Skelton

Abstract:

Alzheimer’s disease (AD) is one of the most common forms of dementia, which is caused by misfolding and aggregation of amyloid beta (Aβ) peptides into amyloid-β fibrils (Aβ fibrils). To disrupt the remodeling of Aβ fibrils, a number of candidate molecules have been proposed. To study the molecular mechanisms of Aβ fibrils remodeling we performed a series of all-atom molecular dynamics simulations, a total time of 3µs, in explicit solvent. Several previously undiscovered candidate molecule-Aβ fibrils binding modes are unraveled; one of which shows the direct conformational change of the Aβ fibril by understanding the physicochemical factors responsible for binding and subsequent remodeling of Aβ fibrils by the candidate molecule, open avenues into structure-based drug design for AD can be opened.

Keywords: alzheimer’s disease, amyloid, MD simulations, misfolded protein

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Authors: Kaining Zhang, Lang Chen, Danyang Liu, Jianying Lu, Kun Yang, Junying Wu

Abstract:

In order to solve the problem of a large amount of simulation and limited simulation scale in the first-principle molecular dynamics simulation of energetic material detonation reaction, we established an artificial intelligence model for analyzing and predicting the detonation reaction mechanism of CL-20 based on the first-principle molecular dynamics simulation of the multiscale shock technique (MSST). We employed principal component analysis to identify the dominant charge features governing molecular reactions. We adopted the K-means clustering algorithm to cluster the reaction paths and screen out the key reactions. We introduced the neural network algorithm to construct the mapping relationship between the charge characteristics of the molecular structure and the key reaction characteristics so as to establish a calculation method for predicting detonation reactions based on the charge characteristics of CL-20 and realize the rapid analysis of the reaction mechanism of energetic materials.

Keywords: energetic material detonation reaction, first-principle molecular dynamics simulation of multiscale shock technique, neural network, CL-20

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Authors: Adam Abate, Elham Rasti, Philip Romero

Abstract:

Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

Abstract:

Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

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Authors: R. O. Ocaya, J. J. Terblans

Abstract:

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C language, molecular dynamics, simulation, embedded atom method

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