Journal of Physical and Theoretical Chemistry
Volume:6 Issue: 4, Winter 2010

Emissions from fossil fuel combustion pose a serious threat to public health and =pose the need for animproved monitoring of polycyclic aromatic hydrocarbons (PARS), a major class of persistent organicpollutants. For this purpose the present study reports an investigation of the electronic structure of Pyrene byuse of different chemical models We also made a comparison between different chemical models.Donor — acceptor disubstituted , entropy , enthalpy and Gibbs free-energy vAll be compared too.The isotropic and anisonopic tensor of the pyrene and derivatives structure were calculated with differentchemical models HP/6-3IG, HF/M1-3 l0, BLYP/6-3 ID, BLYP/6-310. , B3LYP/A3 IG, B3LYP.16-3 I 00 and aswell.

The interaction between the solute and the solsent molecules play a crucial role in understanding the various molecular processes involved in chemistry and biochemistry, so in this work the potential energy of active site of azurin have been calculated in solvent by the Monte Carlo simulation. In this paper we present quantitative results of Monte Carlo calculations of potential energies of active site of azurin in water, ethanol, methanol and gas phase at three temperatures 300, 305,310 K. According to the obtained results, the potential energy of active site conformation is decreased quickly in water and the greater stability in this study is related to at.er and then methanol. It has been found that in different solsent media the highest potential energy value and then the least stability correspond to ethanol and also through increasing the dielectric constant of solvent the structural energy values decreased. Thus, the protein environment, which is often aqueous. aftects the structure. folding dynamic and stability, and, therefore, the functionality of globular proteins. In fact, solvent-protein interactions, together with the interactions between residues in the protein matrix, facilitate the folding process and establishment of intermolecular interactions with other complex systems Furthermore, to be properly folded and fully functional, a protein requires a minimum lesel of hydration.

In this research, the interaction of hexadecyl trimahyl ammonium bromide (HTAB) with enzyme ureasehas been investigated comprehensively at different experimental conditions such as ionic strength, proteinconcentration using ion selective membrane electrode of surfactants. The obtained binding isotherms frompotentiometnc studies have been analyzed by different theories such as Wyman binding potennal.Seatehard diagram, binding capacity concept and Hill equation. The results indicate the aggregation ofurease at concentrations more than I mg/m1 of protein. !mu-easing the ionic strength to I m41, causes todecrease the interaction with mase but increasing the ionic strength to more than I inftl again causes toincrease the interaction. Tlus issue can be due to stability of unease at ionic strength oil rn.M. increasingthe concentration of urease to 3 RIM causes to gradual and regular decreasing of interaction and at higherconcentrations, the intense increase in interaction is resulted. Increasing pH from 6.5 to 9.7 does not creategreat changes at binding isotherms that is due to slight change of dissociation &pee of acidic and basicgroups and third structure of urease at this limit. In all studied cases m comparison with similar case, itshows stronger interaction with urease. This issue is Justifiable according to longer hydrocarbon tail thatincreases its hydrophobic properly that indicates the special role of hydrophobic interactions in interactionsprocess of ionic surfatttuns with proteins.

In this work, we have studied the solvent effects on values of Gibbs free energy, enthalpy. entropy and dipolemoment in spread of solvents around anticancer thug of temreolomide that is an alighting agent. For thispurpose, the quantum mechanic calculations bawd on Hanrertnick theory at the STO-36/3-2Ith levels havebeen done. Moreover, we have compared resulted thermodynamic values in gas phase as well as varioussolvents when surround the Temazolumide molecule We obtained the effects of different dielectric constantson Temozolomide with the myna- self-consistent model reaction field (SCRF) by applying Hartreeffocktheory and also we obtained the effects of temperature on thermodynamic values of Temozolomide in gas phaseand various solvents.

IniB-the main external virulence factor of the bacterium Listeria monueytogenes- contains seven parallelB-strands at its concave face with a patches of five exposed aromatic amino acids as a hot spot for host receptor(Met) binding. For better understanding of energetic and physicochemical pmpendes, (u)folding transition,binding affinity and makmetic shielding censors of JAB-CRP-II-sheet ab hullo computer-aided methods havebeen performed at the Hartree-Fork level. These calculations are based on the influence of solvent polarity aswell as hydrogen bond donor and acceptor strensth of it with respect to the self-consistent reaction field(SCRF) method using Onsager model. The optimized molecule with 6-316(4) basis yet in the as phasewas used as initial input for subsequent liFiSCRT calculations implementing 6-310(d,p) atomic basis set COsimulate the solscnt effect. To gain further insight to solvent effects on aromatic amino acids IIN and 1.0atoms engaged in hydrogen bonding with receptor, NMR studies have been carried out on the basis of gaugeincludingatomic orbital (GIAO) method at HF/6-3ICi (d,p) level of theory HE' calculations obtained with agood agreement by the presented experimental data and predict the most molecule instability in the solventsby low dielectric constants like THE and existence of a cooperaivi among 0-strands. physicochemicallyThere are various potential of hydrogen bond donors and acceptors among this unique, packed and exposedlinearly arrangement of aromatic amino acids that have made it an ideal part for drug design.

A theoretical study of the kinetic and mechanism of 3-aug-Cope rearrangement in gas phase was performed usingDET methods at B3LYP levels of theory with 6-3114iG(d,p) bass set at 298.I5K. Equilibrium moleculargeometries and harmonic vibrational frequencies of the reactant, transition state Did product were calculated. Then,rate constant and activation thermodynamics parameters were calculated and the results showed a fairly goodagreement with experimental results that cited in the reference 25. These calculations indicated that the reactionproceeds through an asynchronous concerted mechanism.

A new simple arid rapid catalytic kinetic method for determination of trace amounts of chromium (110 isdescribed. The method is based on the catalytic effect of chromium (III) on the reduction of Methylene blue byascorbic acid in acidic media. The reaction monitored smectrophotomenically by measuring the decrease ofabsorbance at 664 nm at 25 C. The fixed-time method was used for the first 300 s. Under the optimumconditions, the amount of Cr(111) in the concentration range of 0.5 - 520.0 wg ml_dt (III) can be determined witha limit of detection of 0.09 wg mL- of chromium (111). The relative standard deviations of six replicatemeasurements are 2.8 and 2.1% for 50.0 and 500.0 wg rni.-1 of chromium (III), respectively. The effect ofcertain foreign species upon the reaction rate was investigated for the assessment of the selectivity of themethod The proposed method was successfully applied to the determination of chromium (III) in real sampleswith satisfactory results. The new developed method was found to have fairly goad seleethity, sensitivity,rapidity, reproduceability and simplicity

Nanopartmles have been used as an approach to improve the pharmacodynamic and phannacokinetie propertiesof various drues. Amino acids have been considered to be useful to make such nano particles because ofthocompatithe and biodegradable characteristic. The quantum mechanical method that was chosen to analyze inethio hexa peptide nano ring]. The structure of some peptide nanorrigs as well as their dipole moments andenergies have been studied by quantum chemical calculations within the Ousager self-consistent reaction field(SCRF) model zing a Hartree-Fock method (RHF) at the RIIF/STO-30 (5D-7F). Radius of Gyration, Dipolemoment and Ramachandnm Plot are obtained to analyze the physicochemical characteristics of eyelo hexapeptide nano rings. These rings are studied concerning the utilization as nanovehicles.

In this research, we have studied the structural propenies of water. methanol and ethanol surrounding snidewalledcarbon nanotube (SWCNT) and mixed of them either and we have investigated the solvent effects onthe relative energies and dipole moment values by ming molecular dynamics simulation. We used differentforce field it, deterrnaned energy and other type of geometrical parameters, on the particular SWCNT, becauseof the differences among force fields, the energy of a molecule calculated using two different force fields willnot be the same. In this study difference in force field illustrated by comparing the energy of calculated byusing force fields, MM-F, Amber and OPLS The Quantum Mechanics (QM) calculations were earned out vAththe GAUSSIAN 98 program based on density functional theory (OFT) at B I LYP/3-210 level. In this study,we have comparison between vacuum phase and solvent calculations that considered solvents such as water,methanol, and ethanol and mixed of them. Therefore in this study we investigate polar solvents effects onSWCNT mthin the Onsager self-consistent reaction field (SCRF) model at BILYP/3-21G level and thetemperature effect on the stability of SWCNT in various solvents.

In recent work, thermal energy gaps. AE, it °PUPS gas, Ana; Gibbs free energy gaps, AG.,, between singlet(s) and triplet 0) states of 5.12C3H2C, I m (4 N. P. As and Sb) were calculated and compared with thoseanalogues. MC2113C, (M= CIL N. P. As and Sb) at B3LYIE6-311-NG" level of theory. Our itself showedthat Gibbs free energy gaps. AG, for l uu and 1 p are less than IS and I's, respectively. In contrast, the ACL., for1dd and Is, are more than 1', and I respectively. The AG,., between singlet and triplet states of If and 1'd,were changed in the order: l vt,> I As > 1>1 >1 IN; 1'Sb >1 rcs > 1>Uw, respectively.