Search results for: Atoms in molecules

Authors: S. Heydarian

Abstract:

Proton transfer and hydrogen bonding are two aspects of the chemistry of hydrogen that respectively govern the behaviour and structure of many molecules, both simple and complex. All the theoretical enol and keto conformations of 1,3-diphenyl-1,3- propandion known as dibenzoylmethane (DBM), have been investigated by means of atoms in molecules (AIM) theory. It was found that the most stable conformers are those stabilized by hydrogen bridges.The aim of the present paper is a thorough conformational analysis of DBM (with special attention on chelated cis-enol conformers) in order to obtain detailed information on the geometrical parameters, relative stabilities and rotational motion of the phenyl groups. It is also important to estimate the barrier height for ptoton transfer and hydrogen bond strength, which are the main factors governing conformational stability.

Keywords: Acetylacetone, Atoms in molecules, Dibenzoylmethane, Intramolecular hydrogen bond, Resonanceconjugation

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Authors: Sanaz Gharehzadeh Shirazi, Subira Gharehzadeh Shirazi, Fariba Jafari

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The present article comprises a theoretical study of structures Performat radical (HCO3) with H2O molecule. We make use of ab initio quantum chemical methods. Unrestricted Hartee-Fock (UHF) with the basis set6-311+g(2df,2p) and density functional theory (B3LYP) with the basis set 6-311+g(2df,2p) and also we done atoms in molecules (AIM) theory for them. We have found four stable geometries the PerformatRadical(HCO3) with H2O.

Keywords: Hydrogen binding, Performat Radical, Water, Gaussian, Atoms in molecules (AIM) theory

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Authors: A.Seif, H.Aghaie, K.Majlesi

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A computational study at the level density functional theory (DFT) was carried out to investigate the influences of Si and C-doping on the 14N and 27Al quadrupole coupling constant in the (10, 0) zigzag single ? walled Aluminum-Nitride nanotube (AlNNT). To this aim, a 1.16nm, length of AlNNT consisting of 40 Al atoms and 40 N atoms were selected where the end atoms are capped by hydrogen atom. To follow the purpose, three Si atoms and three C atoms were doped instead of three Al atoms and three N atoms as a central ring in the surface of the Si and C-doped AlNNT. At first both of systems optimized at the level of BLYP method and 6-31G (d) basis set and after that, the NQR parameters were calculated at the level BLYP method and 6-311+G** basis set in two optimized forms. The calculate CQ values for both optimized AlNNT systems, raw and Si and C-doped, reveal different electronic environments in the mentioned systems. It was also demonstrated that the end nuclei have the largest CQ values in both considered AlNNT systems. All the calculations were carried out using Gaussian 98 package of program.

Keywords: DFT, Quadrupole Coupling Constant, Si and CDoping, Single-Walled AlN nanotubes.

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Authors: Pavlo Selyshchev, Samuel Akintunde

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A theoretical approach to consider formation of chemical compound layer at the interface between initial substances A and B due to the interfacial interaction and diffusion is developed. It is considered situation when speed of interfacial interaction is large enough and diffusion of A-atoms through AB-layer is much more then diffusion of B-atoms. Atoms from A-layer diffuse toward B-atoms and form AB-atoms on the surface of B-layer. B-atoms are assumed to be immobile. The growth kinetics of the AB-layer is described by two differential equations with non-linear coupling, producing a good fit to the experimental data. It is shown that growth of the thickness of the AB-layer determines by dependence of chemical reaction rate on reactants concentration. In special case the thickness of the AB-layer can grow linearly or parabolically depending on that which of processes (interaction or the diffusion) controls the growth. The thickness of AB-layer as function of time is obtained. The moment of time (transition point) at which the linear growth are changed by parabolic is found.

Keywords: Phase formation, Binary systems, Interfacial Reaction, Diffusion, Compound layers, Growth kinetics.

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Authors: S. Sobhanian, H. Naghshara, N. Sadeghi, S. Khorram

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The absolute Cu atoms density in Cu(2S1/2ÔåÉ2P1/2) ground state has been measured by Resonance Optical Absorption (ROA) technique in a DC magnetron sputtering deposition with argon. We measured these densities under variety of operation conditions: pressure from 0.6 μbar to 14 μbar, input power from 10W to 200W and N2 mixture from 0% to 100%. For measuring the gas temperature, we used the simulation of N2 rotational spectra with a special computer code. The absolute number density of Cu atoms decreases with increasing the N2 percentage of buffer gas at any conditions of this work. But the deposition rate, is not decreased with the same manner. The deposition rate variation is very small and in the limit of quartz balance measuring equipment accuracy. So we conclude that decrease in the absolute number density of Cu atoms in magnetron plasma has not a big effect on deposition rate, because the diffusion of Cu atoms to the chamber volume and deviation of Cu atoms from direct path (towards the substrate) decreases with increasing of N2 percentage of buffer gas. This is because of the lower mass of N2 atoms compared to the argon ones.

Keywords: Deposition rate, Resonance Optical Absorption, Sputtering.

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Authors: L. Mahdavian, M. Raouf

Abstract:

Three dimensional nanostructure materials have attracted the attention of many researches because the possibility to apply them for near future devices in sensors, catalysis and energy related. Tin dioxide is the most used material for gas sensing because its three-dimensional nanostructures and properties are related to the large surface exposed to gas adsorption. We propose the use of branch SnO2 nanowhiskers in interaction with ethanol. All Sn atoms are symmetric. The total energy, potential energy and Kinetic energy calculated for interaction between SnO2 and ethanol in different distances and temperatures. The calculations achieved by methods of Langevin Dynamic and Mont Carlo simulation. The total energy increased with addition ethanol molecules and temperature so interactions between them are endothermic.

Keywords: Tin dioxide, nanowhisker, Ethanol, Langevin Dynamic and Mont Carlo Simulation.

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Authors: Patrick Maier, Marcus Tönnis, Gudrun Klinker

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Spatial understanding and the understanding of dynamic change in the spatial structure of molecules during a reaction is essential for designing new molecules. Knowing the physical processes in the reactions helps to speed up the designing process. To support the designer with the correct representation of the designed molecule as well as showing the dynamic behavior of the whole reacting system is the goal of our application. Our system shows the spatial deformation of the molecules at every time interval by minimizing the energy level of the molecules. The position and orientation of the molecules can be intuitively controlled by manipulating objects of the real world using Augmented Reality techniques. Our approach has the potential to speed up the design of new molecules and help students to understand the chemical processes better.

Keywords: Augmented Augmented Chemical Reactions, Augmented Reality, chemistry, education.

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Authors: Morteza Farahani, Ahmad Seif, Asadallah Boshra, Hossein Aghaie

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Density functional theory (DFT) calculations were performed to calculate aluminum-27, boron-11, and nitrogen-14 quadrupole coupling constant (CQ) in the representative considered model of (6, 0) boron nitride-aluminum nitride nanotube junction (BN-AlNNT) for the first time. To this aim, 1.3 nm length of BNAlN consisting of 18 Al, 18 B, and 36 N atoms was selected where the end atoms capped by hydrogen atoms. The calculated CQ values for optimized BN-AlNNT system reveal different electrostatic environment in the mentioned system. The calculations were performed using the Gaussian 98 package of program.

Keywords: Nanotube Junction, Density functional, Nuclear Quadrupole Resonance.

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Authors: Z. C. Chang, S. C. Liang

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RF magnetron sputtering is used on the ceramic targets, each of which contains zinc oxide (ZnO), zinc oxide doped with aluminum (AZO) and zinc oxide doped with gallium (GZO). The electric conduction mechanism of the AZO and GZO films came mainly from the Al and Ga, the oxygen vacancies, Zn interstitial atoms, and Al and/or Ga interstitial atoms. AZO and GZO films achieved higher conduction than did ZnO film, it being ion vacant and nonstoichiometric. The XRD analysis showed a preferred orientation along the (002) plane for ZnO, AZO, and GZO films.

Keywords: ZnO, AZO, GZO, Doped, Sputtering

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Authors: Norzita Ngadi, John Abrahamson, Conan Fee, Ken Morison

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Poly (ethylene glycol) (PEG) molecules attached to surfaces have shown high potential as a protein repellent due to their flexibility and highly water solubility. A quartz crystal microbalance recording frequency and dissipation changes (QCM-D) has been used to study the adsorption from aqueous solutions, of lysozyme and α-lactalbumin proteins (the last with and without calcium) onto modified stainless steel surfaces. Surfaces were coated with poly(ethylene imine) (PEI) and silicate before grafting on PEG molecules. Protein adsorption was also performed on the bare stainless steel surface as a control. All adsorptions were conducted at 23°C and pH 7.2. The results showed that the presence of PEG molecules significantly reduced the adsorption of lysozyme and α- lactalbumin (with calcium) onto the stainless steel surface. By contrast, and unexpected, PEG molecules enhanced the adsorption of α-lactalbumin (without calcium). It is suggested that the PEG -α- lactalbumin hydrophobic interaction plays a dominant role which leads to protein aggregation at the surface for this latter observation. The findings also lead to the general conclusion that PEG molecules are not a universal protein repellent. PEG-on-PEI surfaces were better at inhibiting the adsorption of lysozyme and α-lactalbumin (with calcium) than with PEG-on-silicate surfaces.

Keywords: Stainless steel, PEG, QCM-D, protein, PEI layer, silicate layer.

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Authors: D. Bhaskar, N. R. Wadehra, M. Gulati, A. Narula, R. Vishnu, G. Katyal

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With drug resistance becoming widespread in Plasmodium falciparum infections, the development of the alternative drugs is the desired strategy for prevention and cure of malaria. Three drug targets were selected to screen promising drug molecules from the GSK library of 13469 molecules. Using an in silico structure-based drug designing approach, the differences in binding energies of the substrate and inhibitor were exploited between target sites of parasite and human to design a drug molecule against Plasmodium. The docking studies have shown several promising molecules from GSK library with more effective binding as compared to the already known inhibitors for the drug targets. Though stronger interaction has been shown by several molecules as compared to the reference, few molecules have shown the potential as drug candidates though in vitro studies are required to validate the results. In case of thymidylate synthase-dihydrofolatereductase (TS-DHFR), three compounds have shown promise for future studies as potential drugs.

Keywords: Drug resistance, Drug targets, In silico studies, Plasmodium falciparum.

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Authors: Mahasen M. Abdel-Mageed, H. S. Zaghloul

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Annihilations, phase shifts, scattering lengths and elastic cross sections of low energy positrons scattering from magnesium atoms were studied using the least-squares variational method (LSVM). The possibility of positron binding to the magnesium atoms is investigated. A trial wave function is suggested to represent e+-Mg elastic scattering and scattering parameters were derived to estimate the binding energy and annihilation rates. The trial function is taken to depend on several adjustable parameters, and is improved iteratively by increasing the number of terms. The present results have the same behavior as reported semi-empirical, theoretical and experimental results. Especially, the estimated positive scattering length supports the possibility of positronmagnesium bound state system that was confirmed in previous experimental and theoretical work.

Keywords: Bound wave function, Positron Annihilation, scattering phase shift, scattering length.

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Authors: A. Galashev

Abstract:

Absorption spectra of infra-red (IR) radiation of the disperse water medium absorbing the most important greenhouse gases: CO2 , N2O , CH4 , C2H2 , C2H6 have been calculated by the molecular dynamics method. Loss of the absorbing ability at the formation of clusters due to a reduction of the number of centers interacting with IR radiation, results in an anti-greenhouse effect. Absorption of O3 molecules by the (H2O)50 cluster is investigated at its interaction with Cl- ions. The splitting of ozone molecule on atoms near to cluster surface was observed. Interaction of water cluster with Cl- ions causes the increase of integrated intensity of emission spectra of IR radiation, and also essential reduction of the similar characteristic of Raman spectrum. Relative integrated intensity of absorption of IR radiation for small water clusters was designed. Dependences of the quantity of weight on altitude for vapor of monomers, clusters, droplets, crystals and mass of all moisture were determined. The anti-greenhouse effect of clusters was defined as the difference of increases of average global temperature of the Earth, caused by absorption of IR radiation by free water molecules forming clusters, and absorption of clusters themselves. The greenhouse effect caused by clusters makes 0.53 K, and the antigreenhouse one is equal to 1.14 K. The increase of concentration of CO2 in the atmosphere does not always correlate with the amplification of greenhouse effect.

Keywords: Greenhouse gases, infrared absorption and Raman spectra, molecular dynamics method, water clusters.

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Authors: B. Dahiya, K.Batra, V.Prasad

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Artificial atoms are growing fields of interest due to their physical and optoelectronicapplications. The absorption spectra of the proposed artificial atom inpresence of Tera-Hertz field is investigated theoretically. We use the non-perturbativeFloquet theory and finite difference method to study the electronic structure of ArtificialAtom. The effect of static electric field on the energy levels of artificial atom is studied.The effect of orientation of static electric field on energy levels and diploe matrix elementsis also highlighted.

Keywords: Absorption spectra, Artificial atom, Floquet Theory, THz fields

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Authors: V. Rednic, N. Aldea, P. Marginean, D. Macovei, C. M. Teodorescu, E. Dorolti, F. Matei

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The supported Pd catalysts were analyzed by X-ray diffraction and X-ray absorption spectroscopy in order to determine their global and local structure. The average particle size of the supported Pd catalysts was determined by X-ray diffraction method. One of the main purposes of the present contribution is to focus on understanding the specific role of the Pd particle size determined by X-ray diffraction and that of the support oxide. Based on X-ray absorption fine structure spectroscopy analysis we consider that the whole local structure of the investigated samples are distorted concerning the atomic number but the distances between atoms are almost the same as for standard Pd sample. Due to the strong modifications of the Pd cluster local structure, the metal-support interface may influence the electronic properties of metal clusters and thus their reactivity for absorption of the reactant molecules.

Keywords: metal-support interaction, supported metal catalysts, synchrotron radiation, X-ray absorption spectroscopy, X-raydiffraction

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Authors: Bakhtiar Ul Haq, R. Ahmed, A. Shaari, Mazmira Binti Mohamed, Nisar Ali

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The capability of exploiting the electronic charge and spin properties simultaneously in a single material has made diluted magnetic semiconductors (DMS) remarkable in the field of spintronics. We report the designing of DMS based on zinc-blend ZnO doped with Cr impurity. The full potential linearized augmented plane wave plus local orbital FP-L(APW+lo) method in density functional theory (DFT) has been adapted to carry out these investigations. For treatment of exchange and correlation energy, generalized gradient approximations have been used. Introducing Cr atoms in the matrix of ZnO has induced strong magnetic moment with ferromagnetic ordering at stable ground state. Cr:ZnO was found to favor the short range magnetic interaction that reflect tendency of Cr clustering. The electronic structure of ZnO is strongly influenced in the presence of Cr impurity atoms where impurity bands appear in the band gap.

Keywords: ZnO, Density functional theory, Diluted magnetic semiconductors, Ferromagnetic materials, FP-L(APW+lo).

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Authors: Özlen Altun, Zeliha Yoruç

Abstract:

In the present study, the reactions involving 4-bromo-2,6-bis-hydroxymethyl-phenol (BBHMP) and nicotinamide (NA) in the presence of Pd(II) ions were investigated. Optimum conditions for the reactions were established as pH = 7 and λ = 450 nm. According to absorbance measurements, the molar ratio of BBHMP: NA: Pd²⁺ was found to be 1: 2: 2. As a result of physicochemical, spectrophotometric and thermal analyses, the reactions of BBHMP and NA with Pd(II) are complexation reactions and one molecule of BBHMP and two molecules of NA react with two molecules of the Pd(II) ion.

Keywords: Nicotinamide, 4-bromo-2, 6-bis-hydroxymethyl-phenol, Pd(II), spectral analysis, synthesis.

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Authors: Abdulamgid.T. Bouzed, Suleiman. M. Elhamali

Abstract:

The technical realization of data transmission using glass fiber began after the development of diode laser in year 1962. The erbium doped fiber amplifiers (EDFA's) in high speed networks allow information to be transmitted over longer distances without using of signal amplification repeaters. These kinds of fibers are doped with erbium atoms which have energy levels in its atomic structure for amplifying light at 1550nm. When a carried signal wave at 1550nm enters the erbium fiber, the light stimulates the excited erbium atoms which pumped with laser beam at 980nm as additional light. The wavelength and intensity of the semiconductor lasers depend on the temperature of active zone and the injection current. The present paper shows the effect of the diode lasers temperature and injection current on the optical amplification. From the results of in- and output power one may calculate the max. optical gain by erbium doped fiber amplifier.

Keywords: Amplifier, erbium doped fiber, gain, lasers, temperature.

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Authors: Rutanachai Thaipratum

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Free radicals are atoms or molecules with unpaired electrons. Many diseases are caused by free radicals. Normally, free radical formation is controlled naturally by various beneficial compounds known as antioxidants. Several analytical methods have been used for qualitative and quantitative determination of antioxidants, and each has its own specificity. This project aimed to evaluate antioxidant activity of ethanolic and aqueous extracts from the rice paddy herb (Limnophila aromatica (Lam.) Merr.) measured by DPPH and Hydroxyl radical scavenging method. The results showed that averaged antioxidant activity measured in ethanolic extract (µmol Ascorbic acid equivalent/g fresh mass) were 67.09± 4.99 and 15.55±4.82 as determined by DPPH and Hydroxyl radical scavenging activity assays, respectively. Averaged antioxidant activity measured in aqueous extract (µmol Ascorbic acid equivalent/g fresh mass) were 21.08±1.25 and 10.14±3.94 as determined by DPPH and Hydroxyl radical scavenging activity assays respectively.

Keywords: Free radical, antioxidant, rice paddy herb, Limnophila aromatica (Lam.) Merr.

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: Enhanced ideal gas molecular movement, ideal gas molecular movement, model updating method, probability-based damage detection, uncertainty quantification.

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Authors: Hsiao-Wei Wang, Jung-Tang Huang, Chun-Chiang Lin

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Aptamers are useful tools in microorganism researches, diagnoses, and treatment. Aptamers are specific target molecules formed by oligonucleic acid molecules, and are not decomposed by alcohol. Aptamers used to detect Mycobacterium tuberculosis (MTB) have been proved to have specific affinity to the outer membrane proteins of MTB. This article presents a biosensor chip set with aptamers for early detection of MTB with high specificity and sensitivity, even in very low concentration. Meanwhile, we have already made a modified hydrophobic facial mask module with internal rendering hydrophobic for effectively collecting M. tuberculosis.

Keywords: Aptamers, CNTFET, Mycobacterium tuberculosis, early detection.

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Authors: Fred Lacy

Abstract:

Electrical resistivity is a fundamental parameter of metals or electrical conductors. Since resistivity is a function of temperature, in order to completely understand the behavior of metals, a temperature dependent theoretical model is needed. A model based on physics principles has recently been developed to obtain an equation that relates electrical resistivity to temperature. This equation is dependent upon a parameter associated with the electron travel time before being scattered, and a parameter that relates the energy of the atoms and their separation distance. Analysis of the energy parameter reveals that the equation is optimized if the proportionality term in the equation is not constant but varies over the temperature range. Additional analysis reveals that the theoretical equation can be used to determine the mean free path of conduction electrons, the number of defects in the atomic lattice, and the ‘equivalent’ charge associated with the metallic bonding of the atoms. All of this analysis provides validation for the theoretical model and provides insight into the behavior of metals where performance is affected by temperatures (e.g., integrated circuits and temperature sensors).

Keywords: Callendar–van Dusen, conductivity, mean free path, resistance temperature detector, temperature sensor.

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Authors: Shaiemaa, A. Momen, Dalia, A.M. Salem, Emad, M.S. Barakat, Mohamed, S. Salama

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The present study has been conducted to characterize the prophenoloxidase (PPO) system of the desert locust, Schistocerca gregaria following injection of Bacillus thuringiensis kurstaki (Bt). The bulk of PPO system was associated with haemocytes and a little amount was found in plasma. This system was activated by different activators such as laminarin, lipopolysaccharide (LPS) and trypsin suggesting that the stimulatory mechanism may involve an enzyme cascade of one or more associated molecules. These activators did not activate all the molecules of the cascade. Presence of phenoloxidase activity (PO) coincides with the appearance of protein band with molecular weight (MW) 70.154 KD (Kilo Dalton).

Keywords: Schistocerca gregaria, haemolymph, proteins, prophenoloxidase system, phenoloxidase

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Authors: A. A. Vasin, N. V. Klassen, A. M. Likhter

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Water suspensions of in-organic (metals and oxides) and organic nano-objects (chitozan and collagen) were subjected to the treatment of direct and alternative electrical fields. In addition to quasi-periodical spatial patterning resonance-like performance of spatial distributions of these suspensions has been found at low frequencies of alternating electrical field. These resonances are explained as the result of creation of equilibrium states of groups of charged nano-objects with opposite signs of charges at the interparticle distances where the forces of Coulomb attraction are compensated by the repulsion forces induced by relatively negative polarization of hydrated regions surrounding the nanoparticles with respect to pure water. The low frequencies of these resonances are explained by comparatively big distances between the particles and their big masses with t\respect to masses of atoms constituting molecules with high resonance frequencies. These new resonances open a new approach to detailed modeling and understanding of mechanisms of the influence of electrical fields on the functioning of internal organs of living organisms at the level of cells and neurons.

Keywords: Bio-polymers, chitosan, collagen, nanoparticles, coulomb attraction, polarization repulsion, periodical patterning, electrical low frequency resonances, transformations.

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Authors: A. R. Shahani, E. Mahdavi, M. Amidpour

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Hydrogen diffusion is the main problem for corrosion fatigue in corrosive environment. In order to analyze the phenomenon, it is needed to understand their behaviors specially the hydrogen behavior during the diffusion. So, Hydrogen embrittlement and prediction its behavior as a main corrosive part of the fractions, needed to solve combinations of different equations mathematically. The main point to obtain the equation, having knowledge about the source of causing diffusion and running the atoms into materials, called driving force. This is produced by either gradient of electrical or chemical potential. In this work, we consider the gradient of chemical potential to obtain the property equation. In diffusion of atoms, some of them may be trapped but, it could be ignorable in some conditions. According to the phenomenon of hydrogen embrittlement, the thermodynamic and chemical properties of hydrogen are considered to justify and relate them to fracture mechanics. It is very important to get a stress intensity factor by using fugacity as a property of hydrogen or other gases. Although, the diffusive behavior and embrittlement event are common and the same for other gases but, for making it more clear, we describe it for hydrogen. This considering on the definite gas and describing it helps us to understand better the importance of this relation.

Keywords: Hydrogen embrittlement, Fracture mechanics, Thermodynamic, Stress intensity factor.

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Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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A simple adaptive voice activity detector (VAD) is implemented using Gabor and gammatone atomic decomposition of speech for high Gaussian noise environments. Matching pursuit is used for atomic decomposition, and is shown to achieve optimal speech detection capability at high data compression rates for low signal to noise ratios. The most active dictionary elements found by matching pursuit are used for the signal reconstruction so that the algorithm adapts to the individual speakers dominant time-frequency characteristics. Speech has a high peak to average ratio enabling matching pursuit greedy heuristic of highest inner products to isolate high energy speech components in high noise environments. Gabor and gammatone atoms are both investigated with identical logarithmically spaced center frequencies, and similar bandwidths. The algorithm performs equally well for both Gabor and gammatone atoms with no significant statistical differences. The algorithm achieves 70% accuracy at a 0 dB SNR, 90% accuracy at a 5 dB SNR and 98% accuracy at a 20dB SNR using 30d B SNR as a reference for voice activity.

Keywords: Atomic Decomposition, Gabor, Gammatone, Matching Pursuit, Voice Activity Detection.

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Authors: Elias Akoury

Abstract:

Nuclear Magnetic Resonance (NMR) spectroscopy is an indispensable technique used in structure determination of small and macromolecules to study their physical properties, elucidation of characteristic interactions, dynamics and thermodynamic processes. Quantum mechanics defines the theoretical description of NMR spectroscopy and treatment of the dynamics of nuclear spin systems. The phenomenon of residual dipolar coupling (RDCs) has become a routine tool for accurate structure determination by providing global orientation information of magnetic dipole-dipole interaction vectors within a common reference frame. This offers accessibility of distance-independent angular information and insights to local relaxation. The measurement of RDCs requires an anisotropic orientation medium for the molecules to partially align along the magnetic field. This can be achieved by introduction of liquid crystals or attaching a paramagnetic center. Although anisotropic paramagnetic tags continue to mark achievements in the biomolecular NMR of large proteins, its application in small organic molecules remains unspread. Here, we propose a strategy for the synthesis of a lanthanide tag and the measurement of RDCs in organic molecules using paramagnetic lanthanide complexes.

Keywords: Lanthanide Tags, NMR spectroscopy, residual dipolar coupling, quantum mechanics of spin dynamics.

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Authors: Masroor H. S. Bukhari, Z. H. Shah

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The possibility of intrinsic electromagnetic fields within living cells and their resonant self-interaction and interaction with ambient electromagnetic fields is suggested on the basis of a theoretical and experimental study. It is reported that intrinsic electromagnetic fields are produced in the form of radio-frequency and infra-red photons within atoms (which may be coupled or uncoupled) in cellular structures, such as the cell cytoskeleton and plasma membrane. A model is presented for the interaction of these photons among themselves or with atoms under a dipole-dipole coupling, induced by single-photon or two-photon processes. This resonance is manifested by conspicuous field amplification and it is argued that it is possible for these resonant photons to undergo tunnelling in the form of evanescent waves to a short range (of a few nanometers to micrometres). This effect, suggested as a resonant photon tunnelling mechanism in this report, may enable these fields to act as intracellular signal communication devices and as bridges between macromolecules or cellular structures in the cell cytoskeleton, organelles or membrane. A brief overview of an experimental technique and a review of some preliminary results are presented, in the detection of these fields produced in living cell membranes under physiological conditions.

Keywords: bioelectromagnetism, cell membrane, evanescentwaves, photon tunnelling, resonance

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Authors: M. Maimunah, G.A. Froemming, H. Nawawi, M.I. Nafeeza, O. Effat, M.R. Rohayu Izanwati, M.S. Mohamed Saifulaman

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Attachment of the circulating monocytes to the endothelium is the earliest detectable events during formation of atherosclerosis. The adhesion molecules, chemokines and matrix proteases genes were identified to be expressed in atherogenesis. Expressions of these genes may influence structural integrity of the luminal endothelium. The aim of this study is to relate changes in the ultrastructural morphology of the aortic luminal surface and gene expressions of the endothelial surface, chemokine and MMP-12 in normal and hypercholesterolemic rabbits. Luminal endothelial surface from rabbit aortic tissue was examined by scanning electron microscopy (SEM) using low vacuum mode to ascertain ultrastructural changes in development of atherosclerotic lesion. Gene expression of adhesion molecules, MCP-1 and MMP-12 were studied by Real-time PCR. Ultrastructural observations of the aortic luminal surface exhibited changes from normal regular smooth intact endothelium to irregular luminal surface including marked globular appearance and ruptures of the membrane layer. Real-time PCR demonstrated differentially expressed of studied genes in atherosclerotic tissues. The appearance of ultrastructural changes in aortic tissue of hypercholesterolemic rabbits is suggested to have relation with underlying changes of endothelial surface molecules, chemokine and MMP-12 gene expressions.

Keywords: Ultrastructure of luminal endothelial surface, Macrophage metalloelastase (MMP-12), Real-time PCR.

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Authors: K. Massila, R. D. Stein, S. M. Suhaizan, A. A. Azlianor

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A number of mass spectrometry applications are already available as web-based and windows-based systems to calculate isotope pattern and to display the mass spectrum based on the specific molecular formula besides providing necessary information. These applications were evaluated and compared with our new alternative application called Theoretical Isotope Generator (TIG) in terms of its functionality and features provided to prove this new application is working better and performing well. TIG provides extra features than others, complete with several functionality such as drawing, normalizing and zooming the generated graph that convey with the molecular information in a number of formats by providing the details of the calculation and molecules. Thus, any chemist, students, lecturers and researchers from anywhere could use TIG to gain related information on molecules and their relative intensity.

Keywords: Isotope pattern calculator, mass number, massspectrum, relative intensity.

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