The fate of herbicides in soil, and surface and groundwaters is determined by several factors including retention, transformation, and transport processes. Environmental pollutants removed from waters of these chemicals is important for all biologic life. In this study, adsorption of textile dyestuffs or adsorption of pesticides such as bisphenol A, 4-amino nitrophenol, phenoxyacetic acid were examined on PVBCIm. This polymer was obtained by modifying polyvinyl benzyl chloride (PVBC) resin with imidazole. This method, has been extended to chloro methyl group to preparepoly (N-vinyl imidazole) (PVIm) graft chains on crosslinked polyvinyl benzyl chloride (PVBC) polymer. In the aqueous solution the adsorption of organic waste was determined by UV-vis spectrophotometer. For different concentrations of hazardous organic wastes in aqueous solution, Freundlich, Langmuir, and BET isotherms were applied at 25 oC.

In recent years, new materials with advanced properties has attracted great interest in technological applications. The main reason for this is because of the increasing number of people who is dependent of technology-based consumption. Some of the important advanced properties for these new materials are mechanical, barrier and thermal stability. To be successful in preparing a new material with advanced properties, the size of the nanoparticles and its dispersion into the host matrix is extremely important [1-3]. In this study, Carboxymethyl Cellulose (CMC)/silica nano-biocomposite is prepared with a simple chemical method. As a nanofiller silica is used. Iron oxide nanoparticles are embedded into CMC. To reach, well distribution in nano scale of both silica and iron oxide, different amounts of inorganic phase are studied. Distribution of both silica and iron oxide are determined by Scanning Electron Microscopy (SEM) technique. To establish the crystal structure of iron oxide nanoparticles X-Ray Diffraction (XRD) technique is used. Homogenous distribution and The particles appeared dispersed uniformly in CMC. The antibacterial property of the new surface is examined against the gram-negative Escherichia coli. The antibacterial activity of the surface is largely dependent both on the dimension and the dispersion of iron oxide nanoparticles.

Fiber loop ring down (FLRD) spectroscopy is a technique that combines high sensitivity of cavity ring down spectroscopy and elasticity of fiber optic cables. FLRD is a time domain technique that measures optical losses of a light pulse in a fiber loop. In FLRD spectroscopy, detection of a sample is performed by measurement of leaking light at each round trip within an optical cavity. Intensity of leaking light has an exponential decay where it is reduced by absorption of sample and scattering of light. FLRD technique is utilized for characterization of different chemicals and sensing various physical properties such as pressure, temperature, refractive index etc. via remote control. Utilization of FLRD spectroscopy with the aim of trace gas detection has increased in recent years. Different FLRD systems are being improved with this aim in order to increase its sensitivity. Ultimate aim is to be able to perform trace detection at visible region where the chemical sensitivity is higher. Here we present an initial set-up that was designed at 1535 nm and its application on gas and liquid sample detection for trace chemical analysis.

Cornea, the primary refractive element of the eye is a clear, transparent and elastic tissue that acts as a physical barrier between the external environment and the internal ocular elements. Cornea consists of five layers. Its Stroma layer is rich with proteins especially with collagen. Collagen is among the most abundant fibrous proteins and fulfils a variety of mechanical functions. When cross-links between the collagen fibers are weak, cornea will tend to thin and be deformed. This kind of eye disease is called Keratoconus. A unique treatment for Keratoconus is called corneal cross-linking CLX. During the CLX procedure the cornea is exposed to UV-A light and ribofilavin-dextran solution is instilled onto the cornea [1]. This treatment works by increasing collagen cross-links in the Stroma layer. CXL method has some problems which are explained in reference [2]. In this study, temperature and pH level change were examined for different solutions. Nine different solutions with varying concentrations were prepared by using riboflavin, dextran and dextrin substances. Behavior of these solutions at different temperatures and effectiveness of these concentrations according to eyes pH level were investigated. Their absorption and fluorescence spectrum were also investigated in the critical concentration %0.1 w/v of riboflavin [3]. Their diffusion coefficients were found from the ratio of luminescence intensities measurement by using Fick’s Diffusion Law.

The electrophilic carbon atoms of aldehydes can be targets of nucleophilic attack by amines. The end result of this reaction is a compound in which the C=O double bond is replaced by a C=N double bond. This type of compound is known as a Schiff base. In this study some Schiff bases were synthesized from 2-quinoline aldehyde and some aniline derivatives and the molecules were characterized with spectroscopic methods. The pKa values of the molecules calculated with potentiometric methods and DFT calculated methods. The spectroscopic and the potentiometric results were compared with the calculated results.

The mix potassium antimonytitrate with chloride of copper (I) is dissolved in ethyleneglycol and to it increases as seleniruyushchy reagent selenidesulphate sodium. The experimental ware in a teflon ditch is located in the microwave electric oven. Test within 10 hours at 1800? to temperature remains in the furnace. The received deposit is filtered via the glass filter, washed out by the diluted solution of hydrochloric acid, ultrapure water, at last, ethyl alcohol, is dried up at 60-70 0C in vacuum. The exit makes 92-94%. Chemical, thermographic and morphological analyses ?uSbSe2 are executed, and is established that crystals of connection are presented in the form of nanocores.

Amoxicillin, an antibacterial drug, is a part of aminopenicillin family, which is so called broad-spectrum penicillin. In addition to many therapeutic activities, these drugs have several side effects like rash and anaphylaxis. The drug interactions occurring outside the body are categorized as physical or chemical and may occur during formulation, storage as well as while mixing ingredients. The presence of pharmaceuticals in the aquatic environment as well as in drinking water has raised a growing concern in recent years. Among the groups of pharmaceutical compounds of greatest environmental interest are antibiotics due to their extensive use for the treatment of bacterial infections in the whole world. The most dangerous effect of antibiotics is the development of multi-resistant bacterial strains that can no longer be treated with the presently known drugs. Calculations were carried out using the Density Functional Theory DFT/B3LYP/6-31G* levels by using COSMO as the solvation model. For this purpose, possible rections was examined estimately using Gaussian 09 package software.

Nanocomposite is new class of polymer composite whish has nanometer-sized dispersion (1–100 nm) and display excellent properties when compared with conventional composites [1-2]. In this study, we prepared bio-nanocomposite based on organically modified enamel and chitosan using a solvent solution method. The morphology of Chitosan/Modified Enamel bio-nanocomposite were examined by Scanning Electron Microscopy (SEM). This study focused on the predicting the pH dependent swelling behaviour of a hydrogel. The swelling characteristics of Chitosan/Modified Enamel bio-nanocomposite were investigated by swelling experiments. We performed to characterize the swelling behaviour of the in bio-nanocomposite at different pH (3, 4, 7, 10 ve 11) solutions. Chitosan/Modified Enamel bio-nanocomposite reached maximum swelling ratio (%) at pH 11 and the bionanocomposite hydrogel swelling ratio was 4734 at 60 minute. The results showed that the swelling ratio of Chitosan/Modified Enamel bio-nanocomposite depended on pH.

As a member of the benzodiazepines, Clobazam is used in some neurological disorders in CNS including epilepsy, schizophrenia and anxiety. Even though clobazam has been marked as an anticonvulstant since 1984, it was approved for adjunctive therapy in tonicchlonic, complex partial and myoclonic seizures in 2005 (in Canada) [1]. Recently, computational tools have been used to define some important properties such as pharmacokinetics and ADME properties in early stages of drug design [2]. We have tried to produce electronic and structural descriptions of this molecule by using computational methods because the results will be very useful to understand its mechanism of action. All molecular orbital calculations have employed Gaussian 09W [3]. Geometry optimization and frequency calculations have been performed with HF and DFT methods and several basis sets, including 6-31g* and 6-311++g**. In addition to estimates based on Koopmans’s theorem, EPT calculations with the P3 and OVGF approximations have been performed to obtain energy gap values and vertical ionization energies. We also have calculated partial atomic charges by the MPA, NPA, CHELPG, and ESP (which are given for only O and Cl atoms at below) methods to show electronic properties.

Antioxidant compounds in food have proven health-protecting effects. Garlic (Allium sativum) has been cultivated since ancient times and used as a spice and condiment for many centuries. Garlic contains polyphenol and sulphur compounds, which are responsible for its antioxidant activity. In this study the peroxidation of linoleic acid (LA) in the presence of copper (II) [Cu(II)] ions alone and with garlic extract was investigated in aerated and incubated emulsions at 37oC and pH 7. Cu(II)-induced LA peroxidation followed pesudo-first order kinetics with respect to primary (hydroperoxides) and secondary (aldehydes- and ketones-like) oxidation products, which were determined by ferric thiocyanate (FeIII-SCN) and thiobarbituric acidreactive substances (TBARS) methods, respectively [1]. In accordance with theoretical expectations [2], garlic extract showed a distinct dose-dependent antioxidant effect on inhibition of LA peroxidation with respect to hydroperoxide formation, as measured by FeIIISCN colorimetry. Surprisingly, TBARS results were contradictory to this finding, possibly showing the prooxidative effect of garlic extract on secondary product formation during peroxidation. This unexpected result may stem from the generation of reactive sulfur species (RSS) from garlic extract under the Cu(II)-induced oxidizing conditions of the TBARS assay, enhancing (rather than retarding) sulfhydryl and LA oxidation in model systems of lipid oxidation which is better expressed in secondary product formation [3].

Lamotrigine as a voltage- gated sodium channel blocker is used in epilepsy and bipolar disorder [1]. Unlike the other antiepileptics, it has fewer side- effects which make it unique among antiepileptic agents. But there is still the solubility problem about it just like not only antiepileptics but also the other drugs, in pharmaceutical industry. It is estimated that 40% of drug agents have low aqueous solubility [2, 3]. We have investigated in detail to give clear explanation the solubility of Lamotrigine according to its relatedphysicochemical properties. In this context, we have performed solvation calculations for global minimum structure to obtain the thermodynamics about it, in different solvent environment. And we also calculated partial atomic charges by MPA, NPA, CHELPG, ESP methods to show electronic properties. Finally, EPT calculations with P3 and OVGF approximations have been employed to calculate energy gap values. All calculations have been performed by using the Gaussian 03W [4] package program. Isodensity version of Polarized Continuum Model is used to obtain solvation energetics from 6-31g* and 6- 311++g** basis sets both HF and DFT methods.

Ni1-xMnx alloys have been extensively investigated so far, mainly because of their unusual physical properties [1]. Most obvious and common behavior of Ni1-xMnx alloy is the sequence of magnetic phase transitions from paramagnetic at higher temperature, to ferromagnetic-like at intermediate temperatures and spin-glass-like properties with decreasing temperature. These behaviors are believed to originate from the competing interactions between ferromagnetic Ni–Ni, Ni–Mn and antiferromagnetic Mn–Mn pairs. Some similar work has been shown that the magnetic states and the electrical properties are significantly changed, especially at low temperatures, by the addition of a few atomic per cent of nonmagnetic Ti impurities to NiMn alloy. Magnetic measurements have been carried out for both Ni72Mn27Ti1 and Ni72Mn25Ti3 sample by using vibrating sample magnetometer (VSM). As can be seen from Fig.1, the value of magnetization sharply increases with the external magnetic field strength at low field region and, however, it can not reach a saturation state yet in the presence of a relatively strong magnetic field of even 5 kOe. The high field side of the curves are almost lineer with the external field. The measured value of saturation magnetization decreases with increasing temperature as well. The non-saturated magnetization suggests the existence of strong antiferromagnetic inter-cluster interactions mixed with ferromagnetic interactions inside the clusters [2,3,4]. By increasing the applied field, the ferromagnetic part tends to saturate, whereas the antiferromagnetic part increases linearly. Fig. 2 displays the M-T curves of the sample at the applied field of 100 Oe, respectively. It is found that for the ZFC curve start to increase at critical temperature of 90 K showing a phase transition. Then with decreasing temperature, exhibits a maximum at around 16K and start to decrease below this temperature. The decrease in magnetization below this temperature may indicate that there are strong antiferromagnetic inter-cluster interactions between the particles [2,4,5].

This study deals with the electronic configuration of Co ions in misfit Ca3Co4O9 system at high temperature. The magnetic behaviour of this system shows an anomaly around 700 K. It is believed that this anomaly is caused by spin state transitions of Co2+, Co3+ and Co4+ ions in the system. A detailed study of the symmetry properties of the wave functions of Co ions in an octahedral environment indicates that Co4+ ion prefers high spin configuration earlier than Co3+ ions. On the other hand the ligand field splitting of d orbitals in an octahedral environment shows that high spin configuration of Co3+ ions should be populated earlier than the high spin state of Co4+ ions.

In this study, certain theoretical properties of six flavonoles-glucosides, and their tautomers (Table 1) such as stability, reactivity, geometry, nucleophilicity, possible Hbonds, and energy have been calculated by MOPAC2012 packet program [1] at the Restricted Hartree-Fock level using both PM6 and PM7 semi-empirical SCF-MO methods to understand the basic principles to understand their antioxidant behaviors [2].

Oxidative C–H bond activation is of utmost importance in the context of converting small hydrocarbons to alcohols as an alternative to fossil fuel consumption. Despite decades of continued research that utilized transition metal compounds, only a limited number of simultaneous O2 and C–H activation processes are available and it is still challenging to harness alkanes more directly, efficiently and cleanly by using low cost catalysts under mild conditions.[1] In this study, we present a Density Functional Theory analysis (at B3LYP/cc-pVTZ level of theory) reaction mechanisms of methane to methanol conversion with Fe(II)-bispyrazolpyridine (Fe(II)bpp). Structural, energetic, and electronic parameters are reported for the species in the proposed mechanism given in Figure 1.

In this study carboxymethyl cellulose (CMC) reinforced by silica at concentrations from 2 to 15(w/w) have been prepared to investigate the optimal physicochemical properties. The morphological structural and thermal properties of the CMC/ZnO-silica nanobiomaterials were studied to analyze size-dependent interfacial properties and reactivity. X-ray diffraction (XRD) technique was used to characterize the crystallographic structure of the nano- biomaterial. XRD results showed that the silica and ZnO were homogenously dispersed in the CMC matrix. Scanning electron microscopy (SEM) was used to evaluate the ZnO nano particle settlement on silica surface. The thermal stability of CMC and the novel nano-biomaterial was investigated by thermal gravimetric analysis (TGA). The thermal stability of the nano-material was improved systematically with increasing amounts of silica, up to a loading of 10 wt %. The hardness and the elastic modulus were gradually enhanced with increasing silica concentration.

In this study, enthalpy (?H), heat formation (?Hf), entropy (?S), HOMO and LUMO values and dipole moments, possible H-bonds values belong to diabetes (D), cholesterol (K) and blood pressure (T) drugs (Table 1), and the binary interactions of the molecules have been calculated by MOPAC2012 packet program [1, 2] at the Restricted Hartree-Fock level using both PM6 and PM7 semi-empirical SCF-MO methods.Product stabilities were calculated for products formed the binary interaction by using ?G and ?Gf values. The most stable products were K2-D1 both for PM6 and PM7at T=298 K, at T=310 K, K2-D1 for PM6 and K2-D1, K3-D1 for PM7 using ?Gf values; D1-T3 was at T=298K and 310K for PM6 and PM7, K3-D1 and D1-T3 were both at T=298K and 310K for PM6 and PM7 by ?G values, have been calculated.

In this study, certain theoretical properties of three N-(a,ß-Unsaturated acyl)sulphonamides (3) and seven reactants; Sulfonamides(2) with N-(a,ß-unsaturated acyl)benzotriazoles(1) and a,ß-unsaturated carboxamides(4) with sulfonylbenzotriazoles(5) (Table 1) , calculated in Gaussian09 program [1] using DFT method at B3LYP/6-311++g(d,p) level of theory. The theoretical data was then compared with that of certain experimental results [2]

The Beckmann rearrangement (BKR) is an acid-induced rearrangement to produce amides and lactams from oximes. However, the traditional reagents used in the experimental studies suffer from several problems including poor reactivity, hazardous byproduct formations. In a recent study on BKR by Yadav et al., the product was obtained with a better yield and high stereoselectivity with an efficient organocatalysis process. (1) In the study, cyclopropenones are used as an organocatalyst that are the precursors of the cyclopropenium ion. The stability of these three membered ring structures derived from the delocalization of the two-pi electrons over three 2p orbitals and possessing an ionic charge that leads to high reactivity towards anions. An organocatalytic mechanism via formation of a Meisenheimer complex is suggested since neither imidoyl chloride nor 2,3- diphenylcyclopropenone were observed during the experiment. After a short while Lambert et al. published a study similar to Yadav et al. based on the organocatalyzed BKR with cyclopropenium ion and its products. (2) In the study, experiments were conducted at room temperature and in the presence of nitromethane or acetonitrile solvents. Lambert et al. proposed two different mechanisms based on experimental results: organocatalytic and self-propagating mechanisms as distinct from the previous studies. Another study by Lambert et al. proposed that the reaction may be self-propagating rather than organocatalytic. The mechanism of the organocatalytic BKR is not clarified completely. In this theoretical study, the role of the cyclopropenium ion is investigated and the different mechanisms are designed based on the experimental findings. The geometrical structures of all stationary points in the energy profile are optimized at the M062X/6-31+G(d ,p) level of theory including solvent effects. The alterations in the oxime and cyclopropenone ring substitutents should have an the impact on the efficiency of the reaction. Therefore different oximes and cyclopropenes are studied. (Scheme 1) The ultimate aim of this study is to elucidate the mechanism of the cyclopropenium activated BKR reactions with a computational approach.

Copper and copper based alloys are of considerable importance as they form the backbone of modern industries. Brass has been widely used for shipboard condensers, power plant condensers and petrochemical heat exchangers [1]. Thiadiazoles which are important compounds in many fields were reported earlier as corrosion inhibitors for metals and their alloys [2-8]. Recently, Joseph Raj at al. [9] was experimentally investigated the inhibition efficiencies of three amino thiadiazole derivatives for brass in natural seawater as shown in Figure 1. The relationships between the quantum chemical parameters and corrosion inhibition of those compounds have not been studied yet. In this study, corrosion inhibition efficiencies of three amino thiadiazole derivatives namely 2-amino-5-etil-1,3,4-thiadiazole (AETD), 2-amino-5-etiltiyo-1,3,4-thiadiazole (AETTD) and 2-amino-5-ter-butil-1,3,4-thiadiazole (ATBTD) as corrosion inhibitors on brass known as copper alloy in both gas and water phase were investigated by using B3LYP/6-31G(d,p) and B3LYP/6-31++G(d,p) basis sets by DFT method. Quantum chemical parameters such as the highest occupied molecular orbital energy (EHOMO), the lowest unoccupied molecular orbital energy (ELUMO), energy gap (?E= ELUMO - EHOMO), sum of the total negative charge (TNC), electronegativity (?), global hardness (?), softness (?), the fraction of electrons transferred (?N) and proton affinity (PA) were calculated. Furthermore, the interaction energies of the investigated amino thiadiazole derivatives with the copper metal were obtained. The effect of substituent types and its positions on the thiadiazole ring were investigated for all structures. As a results, the inhibition efficiency of investigated amino thiadiazole derivatives was observed to increase with increasing the electron donor characteristic of the substituted groups. A good correlation was found between the quantum chemical parameters and experimental inhibition efficiencies of the investigated amino thiadiazole derivatives.

In this study, all acidity constants of six azo dyes derived from 4-(phenyldiazenyl)benzene-1,3-diol have been calculated by DFT method with Gaussian09 [1] program (B3LYP/6-311++G(d,p)) [2].The theoretical data has compared with those of experimental ones [3]. Then, proton gain and loose centers of these molecules have been determined. It has been indicated that first protonation is on N1 nitrogen with correlation constant R2=0,9996. First deprotonation is on the hydrogen binding O1 with the correlation constants (R2=0, 9957) and second deprotonation is on the hydrogen binding O1 and O2 with R2=0, 9715.

Antioxidant compounds in food play an important role as health-protecting factors. Scientific evidence suggests that antioxidants can reduce the risk for chronic diseases including cancer and heart disease. The main characteristic of an antioxidant is its ability to trap free radicals. Highly reactive free radicals and oxygen species are present in biological systems from a wide variety of sources. These free radicals may oxidize nucleic acids, proteins, lipids or DNA and can initiate degenerative disease. Antioxidant compounds scavenge free radicals such as peroxides, hydroperoxides or lipid peroxyls and thus inhibit the oxidative mechanisms that lead to degenerative diseases. Chromone derivatives are abundant in nature and exhibit a wide range of pharmacological activity like anti-bacterial, anti-fungal, anti-cancer, anti-oxidant, anti-HIV, anti-ulcers [1,2]. Schiff bases of 3-formyl chromone also have a variety of applications in biological, clinical and pharmacological areas [3,4]. In this work, 3-((3-hydroxypyridin-2-ylimino)methyl)-4Hchromen-4-one (I) and 3-(-(2-mercaptophenylimino)methyl)-4H-chromen-4-one (II)[5] are chosen to investigate the capacity of their antioxidant activity. In order to explain the antioxidant performance of these compounds, the BDE and electronic properties such as HOMO and LUMO energies, IP, hardness and sofness were computed and in detail.

Oxidative C–H bond activation is of utmost importance in the context of converting small hydrocarbons to alcohols as an alternative to fossil fuel consumption.[1] Despite decades of continued research that utilized transition metal compounds, only a limited number of simultaneous O2 and C–H activation processes are available.[2] It is still an immense challenge to convert methane into methanol by using low cost catalysts under mild conditions. Herein, we report a Density Functional Theory analysis (utilizing the B3LYP functional) of the methane to methanol conversion paths (Figure 1) by Fe(II)[2,6-bis(2-pyridyl)pyridine] (Fe(II)[tpy]) complex. Possible intermediates and transition structures for the proposed paths were located. Structural, energetic and electronic properties of the reaction intermediates were corroborated.

Heat shock protein Hsp70 is a chaperon which helps folding of other proteins. It consists of two domains: a nucleotide binding domain where ATP or ADP binds and a substrate binding domain where the protein to be folded binds [1]. In the presence of ATP, the substrate affinity of Hsp70 is low. Binding of a substrate triggers ATP hydrolysis. In ADP bound form, the substrate affinity is high [1]. The allosteric communication between the two domains is mediated by a linker. The ATPase activity is pH dependent, the optimum pH being around 7.5 [2]. This study aims at understanding the role of the linker in triggering the ATP hydrolysis and the origin of the pH dependence of the reaction using molecular dynamics simulations. It is experimentally known that an Hsp70 construct containing only the nucleotide binding domain and the linker has the same ATPase rate as the full length Hsp70. Hence, in order to reduce the computational cost, simulations have been made on a truncated Hsp70 structure. Several simulations with different nucleotide states (ATP bound, ADP bound or nucleotide free) and with different starting geometries have been carried out in order to determine possible positions of the linker and its effect on the active site arrangement. Moreover, pKa values of some important residues inside or near the active site [3, 4] have been calculated via thermodynamic integration simulations. Thermodynamic integration simulations indicate that Asp194 and Asp201 have elevated pKa values, suggesting that these residues may be protonated at pH 7.5. Asp8 and Glu171 have lower pKa values, hence are probably unprotonated. Simulations with different protonation states of Asp194 and Asp201 have been carried out. It has been observed that the protonation states of these residues affect the conformational behavior of Hsp70.

The aim of this study is to comprehend the mechanism of the oxidative decomposition of phenylalanine (the simplest aromatic amino acid) by transition metals, in particular cobalt, using quantum mechanical tools. All the ground and transition state structures are optimized using the density functional method M06-2X. Additional calculations have been carried out using M06. Recently, a couple of works for profiling the transcriptomic data of the yeast Saccharomyces cerevisiae when exposed to transition metals, such as cobalt and nickel were done by Çakar and co-workers [1, 2]. According to their results, the cobalt-resistant mutants had a tendency to reduce the amount of aromatic amino acids, suggesting that Co3+, but not other metals, reacts specifically with aromatic amino acids, yielding harmful products. Although the in vitro decomposition of amino acids has been considered in numerous studies in the literature, the mechanism and intermediates formed during the reaction are not clear. The reactions use oxidizing agents such as diperiodatocuprate(III) in alkaline medium, or Mn3+ and its hydroxide form (Mn(OH)2+) in sulfuric acid medium [3, 4]. But the reaction of Co3+ with phenylalanine was not studied. In this study, it has been shown that cobalt (III) ions are powerful oxidizing agents against aromatic amino acids. Our study has revealed several pathways of the decomposition reaction of zwitterionic phenyl alanine at neutral pH and the effect of the Co3+ ion on the decomposition reaction. It was shown that the oxidation of phenylalanine by a Co3+ ion results in decarboxylation and deprotonation of phenylalanine. The presence of the aromatic ring facilitates the redox reaction. Then, oxidation by a second Co3+ in concert with the nucleophilic addition of an OH- ion leads to a pathway that yields phenyl acetaldehyde. A different pathway may proceed through oxidation by two more Co3+ ions and yield phenylacetamide. But this pathway has a higher activation free energy. Another possible decomposition pathway yielding phenylpyruvate also requires a considerably high reaction activation free energy. The reactions of Fe3+ and Ni3+ with phenylalanine have also been investigated. It has been found that these two transition metal ions are not suitable for the reactions mentioned above.

The crystal structure of the voltage-gated bacterial Nav channel obtained from Arcobacter butzleri fortunately [1]. Voltage-gated sodium channels are very important due to the onset of action potentials. Molecular dynamics modelling has been conducted to understand the structure-function relationship for this channel (as shown in figure 1). Using free energy methods, energetics of ion binding is studied and the binding energies and positions were obtained for Na+ ions in the filter. It has been known form the experimental data that Nav and Cav channels are similar and Ca++ ions are permeating in the Nav channels. A potential of mean force calculation is performed for Ca++ ion through the channel axis of the Nav. As a result of this study we observed Ca++ ions have a higher binding affinity than that Na+. Based on these, we studied the potential of mean force for a Na+ ion in case of a Ca++ ion in the filter of the channel. We concluded that if a single calcium ion binds to the specific location of the selectivity filter of the channel, it blocks sodium permeation through sodium channel by providing high energy barrier where the calcium locate in the selectivity filter.

Voltage-gated calcium channels are the primary mediators of depolarization-induced calcium entry into neurons [1]. While calcium channels are of critical importance to brain function, their inappropriate expression or dysfunction gives rise to a variety of neurological disorders, including, pain, epilepsy, migraine, and ataxia. Molecular dynamics methods are the only physically valid methods for studying the structure function relations in ion channels. Applications of these methods to sodium and calcium channels are presented, which illustrate the multi-ion nature of the permeation mechanism in selective biological channels (as shown in Figure 1). In this study, we present binding energies of single and multi-ion Na+ to the Ca++ channels. Furthermore we interpret binding energies for constructing structure-function relationship of this channel.

Nicotinic Acetylcholine Receptors (nAChR) play an important role in drug discovery such as analgesics. Alpha-conotoxin SI (SI) is a 13-aminoacide peptide which exists in the venom of sea cone shell. It is crucial to investigate theinteraction of such peptides for discovering novel drugs. It is almost impossible to investigate the molecular interactions using experimental techniques. At this stage, computational studies such as molecular dynamics (MD) simulations are used to demonstrate such interaction mechanisms. A refined structure for nAChR (Figure 1) was published by Unwin N. in 2005 [1]. We have carried out docking and MD simulations using HADDOCK and NAMD software packages respectively. We show that our MD studies are in agreement with the previous experimental studies [2,3] which present the most possible binding sites and interaction mechanism of nAChR and SI from Potential of Mean Force calculations using a cost-efficient approach.

The non-Newtonian viscosity of atactic and syndiotactic polystyrenes from 200 to 300°C temperature range at various pressures is described well using our recently proposed YDT (Yahsi-Dinc-Tav) and the Cross models [1]. The Pressure-Volume-Temperature (PVT) data of atactic and syndiotactic PSs are fitted to the Simha-Somcynsky equation of state (SS) [2], to calculate the characteristic parameters, such as P* V*, T* and the hole fraction. The relationships among PVTh values are elucidated both with the Simha-Somcynsk y Hole Theory and the previously obtained various Tait equations. The application of the linear dependency of our derived quantities; zero shear and constant shear-rate viscosities with hand Tdependent “thermo-occupancy” function (Yh) leads to extract novel conclusions on the differences between both types of PSs. In particular, as given in Figure 1, the viscoholibility (the derivative of the logarithm ofviscosities) decreases with the increasing hole fraction,h, computed from the SS theory.

Fe-HPCD is a non-heme extradiol enzyme that operates in the oxidative ring opening pathways of aromatic compounds.[1,2] Recent studies showed that the proton transfer to afford 3 or 4 from 0 (Figure 1) is assisted by an His200 residue that is lying in the secondary sphere of HPCD active site.[3,4] Thus, the main role of His200 is acting as a Brønsted base. Herein, we present a Density Functional Theory analysis of the energetics of a modified first coordination shell with the objective of mimicking the role of His200 by incorporation of various functional groups on one of the imidazole rings (Figure 1). The aim is to create a proton transfer agent that is adequate in terms of thermodynamic and kinetic parameters in comparison with the native protein environment. Figure 1 shows the reaction mechanism and possible functional groups capable to act as a proton shuttle.

Water and oil repellencies of flat films are crucial properties of solid materials and some biomimetric surfaces that significantly depend on surface topography and chemical compositions [1,2]. The surface wettability is expressed indirectly by the contact angle (CA) measurements of a specific liquid droplet on these surfaces [1-4]. However, in practical systems, measurement of only equilibrium CA (?e) is not enough to explain polymer surface characteristics, so advancing (?a), receding (?r) CA’s and thus the contact angle hysteresis (CAH= ?a – ?r) are required to accurately characterize the dewetting properties of the surfaces [1-9]. CAH of a surface is strongly affected from surface chemical heterogeneity and roughness. In addition, the relationship between the equilibrium and dynamic states (work of adhesion, Wa and CAH) is also an important parameter for the characterization of solid surfaces. Basically, the estimate of drop movement on a surface can be represented by Wa values, i.e., a higher Wad value causes a higher tendency of the droplet to stick on the tilt surface. In this study, the oil repellencies of flat perfluoroethyl alkyl methacrylate-styrene (Zonyl-TM-S) random copolymers, which were synthesized in a CO2-expanded monomer medium at 250 bar pressure and 80 oC were investigated with various perfluoroethylalkyl contents. Flat and transparent copolymer surfaces were formed by using dip-coated on glass slides from THF as solvent. The increase in the perfluoromethacrylate content of the flat copolymers resulted in a decrease of the total surface free energy of the flat copolymer surfaces from 19.0 to 14.2 mJ/m2. The oil repellencies of (Zonyl-TM-S) copolymers in the terms of contact angle hysteresis was compared with perfluoroethyl alkyl methacrylate-methyl methacrylate copolymer (Zonyl-TM-ran-MMA) by using oil drops with varying surface tensions between 20.9 mN/m and 26.9 mN/m. The effect of liquid surface tension and wt.% content of Zonyl-TM on oleophobicities of the surfaces were also examined. Increase in hydrocarbon chain lengths also caused an increase in the measured CA values due to the weaker adhesion interactions between the liquid drop and the solid surface. Increase in wt.% Zonyl-TM content of the copolymers resulted in a decrease in Wa values due to the increase of fluorine atoms in copolymer surfaces. The relationship between ( r a ) cos? = cos? - cos? and Wa values, liquid surface tensions and also perfluoro alkyl wt.% content of the copolymer were also investigated. Furthermore, the CAH and oil repellency differences between the p(Zonyl-TM-ran-S) and p(Zonyl-TM-ran- MMA) thin copolymer films with similar Zonyl-TM contents were also compared within this work. An increase was found in CAH values with the increase of hydrocarbon liquid chain length and thus liquid surface tension. This is due to the increase in cohesion interactions between liquid molecules and resulted in a decrease in adhesion interactions between the solid surface and the liquid drop.

Hsp70 is a 70 kDa chaperone protein which consist of a 45 kDa N-terminal ATPase domain and a 25 kDa C-terminal substrate binding domain [1]. A linker containing a conserved VLLL sequence connects the two domains and functions in allosteric communication between them [2]. When ATP is bound, the affinity of Hsp70 to substrates, which are misfolded proteins, is low. Upon substrate binding, ATP is hydrolyzed into ADP and the affinity to the substrate increases. Exchange of ADP with an ADP causes the release of the substrate and the new turnover begins [1]. In this study, N-terminal ATPase domain is studied to determine the ATP hydrolysis mechanism of the protein. QM/MM ONIOM method with M062X for QM level and AMBER force field for the MM level is used in this study. In general, phosphate hydrolysis reactions can take place either through an associative or a dissociative mechanism depending on the environment. Therefore, both mechanisms are tested in order to identify lowest energy pathway [3]. Some amino acids in the active site may potentially act in acid/base catalysis. To test this hypothesis, proton transfer from K70, D194 or D201 to ATP is investigated.

Accurate state-to-state quantum wave packet calculations of integral cross sections for the title reaction are presented. Calculations are carried out on the best available ground 12A global adiabatic potential energy surface of Deskevich et. al.[1]. Converged state-to-state wave packet reaction cross sections; with the DCl v=0, j=0-1; v=1, j=0 reagent have been calculated for the collision energy range from threshold up to 0.5 eV. Accurate product vibrational and rotational distributions of cross sections have been calculated at selected collision energies. State-to-state and total initial-state resolved rate constants of the title reaction have been calculated in a temperature range of 100-300 K. The present accurate calculations at v=0, j=0, J=0 show noticeable differences; with previous calculations for the F+HCl reaction. Assuming the reaction coordinate in the F-Cl distance and to estimate the zero point energy in the orthogonal coordinate we have calculated the bound states along the reaction path for frozen F-Cl distance to interpret the results.

Photoinduced electron transfer systems have optical applications such as sensory photoreceptors and light-emitting diodes. The photonic energy which is harvested by an antenna is transformed into ground state chemistry utilizing photoinduced electron transfer or photochemical bond reorganization [1]. Amino acids often possess particular properties, such as weak van der Waals and hydrogenbonds, wide transparency ranges in the visible regions and zwitterionic nature of the molecules which are very important in materials science [2]. In order to be able to optimize the efficiency of organic optical devices, it is an advantage to understand completely the physical behaviour of compounds in gas phase and in solution. We have studied geometrical structure, electronic structure and optical excitation of pyrene(Py)/1-hydroxypyrene (PyOH) with aromatic amino acids in vacuum and in water using DFT and TD-DFT calculations. The density functional theory (DFT) computations have been performed at ?B97XD/6-31G(d,p) level using Gaussian 09 program [3]. Pyrene and hydroxypyrene were chosen as molecular antenna and aromatic amino acids were chosen as electron donors. Our results show that more stable complexes are formed in vacuum. Tryptophan (Trp) complexes are the most stable among all optimized complexes. Significant geometrical changes have been observed for the optimized complexes between gas phase and water. Pyrene/hydroxypyrene-aminoacid interactions via p-p stacking promote the photoinduced transfer reactions. Calculated HOMO-LUMO energies confirm that charge-transfer occurs between the molecules. The most significant charge transfer is observed for Trp complexes between HOMO-1 and LUMO. It is concluded that the lowering of highest occupied orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap appears to be cause of its enhanced charge transfer.