Force Field Calculations Research Articles

Capturing the H2–Metal Interaction in Mg-MOF-74 Using Classical Polarization

Grand canonical Monte Carlo (GCMC) simulations of H2 sorption were performed in Mg-MOF-74, a metal–organic framework (MOF) that displays very high H2 sorption affinity. Experimental H2 sorption isotherms and isosteric heats of adsorption (Qst) values were reproduced using a general purpose materials sorption potential that includes many-body polarization interactions. In contrast, using two models that include only charge–quadrupole interactions failed to reproduce such experimental measurements even though they are the type normally employed in such classical force field calculations. Utilizing the present explicit polarizable model in GCMC simulation resulted in a Mg2+–H2 distance of 2.60 Å, which is close to a previously reported value that was obtained using electronic structure methods and comparable to similar experimental measurements. The induced dipole distribution obtained from simulation assisted in the characterization of two previously identified sorption sites in the MOF: the Mg2+ ions and the oxido group of the linkers. The calculated two-dimensional quantum rotational levels for a H2 molecule sorbed onto the Mg2+ ion were in good agreement with experimental inelastic neutron scattering (INS) data. Although the H2–metal interaction in MOFs may be thought of as a quantum mechanical effect, this study demonstrates how the interaction between the sorbate molecules and the open-metal sites in a particular highly sorbing MOF can be captured using classical simulation techniques that involve a polarizable potential.

Self-assembled supramolecular hetero-bimetallacycles for anticancer potency by intracellular release.

Two new tetracationic hetero-bimetallacycles, compounds 4 and 5, have been constructed from an N,N'-bis(4-(pyridin-4-ylethynyl)phenyl)pyridine-2,6-dicarboxamide ligand (1), and cis-blocked complexes [M(dppf)(OTf)2 ] (dppf=1,1'-bis(diphenylphosphino)ferrocene; OTf=trifluoromethanesulfonate; M=Pd (2), Pt (3)) in CH3 NO2 /CH2 Cl2 (1:1) solvent. Both complexes were isolated with adequate yields as triflate salts and were then characterized using (1) H, (13) C, and (31) P NMR spectroscopy, elemental analysis, UV/Vis spectroscopy, and high-resolution electrospray mass spectrometry (HR-ESMS). The molecular structure of 4 was determined by molecular mechanics force-field calculations. The cytotoxic effect of both new complexes were analyzed against T98G (brain tumor), KB (head and neck cancer), SNU-80 (thyroid cancer), and HEK-293 non-malignant cell lines. The cytotoxicity of complexes 4 and 5 were found to be considerably more effective against cancer cells than reference drug cisplatin. Annexin-V/PI staining, caspase-3/7 activity, and the reduction in mitochondrial membrane potential justify a significant level of apoptosis in complex-treated cells.

Synthesis, crystal growth, thermal, electronic and vibrational spectral studies of 1-(4-Bromophenyl)-3-(3,4-dimethoxy-phenyl)prop-2-en-1-one: A density functional theory study

A new chalcone derivative, 1-(4-Bromophenyl)-3-(3,4-dimethoxy-phenyl)prop-2-en-1-one (DMBC) was synthesized and single crystals were grown by slow evaporation technique. The FT-Raman and FT-IR spectra of the sample were recorded in the region 3500–50cm−1 and 4000–400cm−1 respectively. The spectra were interpreted with the aid of normal coordinate analysis, following structure optimizations and force field calculations based on density functional theory (DFT) at the B3LYP/6-31G(d,p) level of theory. Normal coordinate calculations were performed using the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between the observed and calculated wavenumbers. DMBC is thermally stable up to 265.0°C and optically transparent in the visible region. The total electron density and molecular electrostatic potential surfaces of the molecules were constructed by Natural Bond Orbital analysis using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron+nuclei) distribution, molecular shape, size, and dipole moments of the molecule. The electronic properties, HOMO and LUMO energies were measured.

Antiviral atropisomers: conformational energy surfaces by NMR for host-directed myxovirus blockers.

Biologically active organic molecules characterized by a high single bond torsional barrier generate isolable isomers (atropisomers) and offer a unique stereochemical component to the design of selective therapeutic agents. The present work presents a nanomolar active inhibitor of myxoviruses, which most likely acts by blocking one or more cellular host proteins but also, serendipitously, exhibits axial chirality with an energy barrier of ΔG((++)) ≥30 kcal/mol. The latter has been probed by variable temperature NMR and microwave irradiation and by high level DFT transition state analysis and force field calculations. Full conformational profiles of the corresponding (aR,S) and (aS,S) atropisomers at ambient temperature were derived by conformer deconvolution with NAMFIS (NMR Analysis by Molecular Flexibility In Solution) methodology to generate seven and eight individual conformations, each assigned a % population. An accurate evaluation of a key torsion angle at the center of the molecules associated with a (3)JC-S-C-H coupling constant was obtained by mapping the S-C bond rotation with the MPW1PW91/6-31G-d,p DFT method followed by fitting the resulting dihedral angles and J-values to a Karplus expression. Accordingly, we have developed a complete conformational profile of diastereomeric atropisomers consistent with both high and low rotational barriers. We expect this assessment to assist the rationalization of the selectivity of the two (aR,S) and (aS,S) forms against host proteins, while offering insights into their divergent toxicity behavior.

Structures and properties of gallium-MOFs with MIL-53-topology based on aliphatic linker molecules

Employing gallium nitrate and one of the aliphatic dicarboxylic acids trans-1,4-cyclohexanedicarboxylic acid (H2C8H10O4) or (+)-camphoric acid (H2C10H14O4), respectively, two new metal–organic frameworks exhibiting the MIL-53-topology were synthesised in N,N-dimethylformamide. All structural characterisations were carried out based on Powder-XRD data using a combination of structural relationship, force-field calculations and Rietveld refinement. The compound based on camphoric acid [GaOH(C10H14O4)] or Ga-MIL-53-Cam (1) crystallises in the polar orthorhombic space group P212121 (a=14.0453(3), b=12.0124(3), c=6.7658(2)Å) . Ga-MIL-53-Cam exhibits an unporous dense framework which is stable up to 280°C in air. The second compound [GaOH(C8H10O4)]·0.5DMF (2) or Ga-CAU-13-lp (lp stands for large pore) crystallises in the triclinic space group P-1 (a=6.7114(2), b=10.3019(3), c=9.6265(2)Å, α=110.743(2), β=106.883(3), γ=94.679(3)°). While this compound shows no porosity towards nitrogen at 77K, water molecules can be adsorbed into the pores upon exposure to air after thermal removal of the DMF molecules. The thus obtained [GaOH(C8H10O4)]·H2O (3) or Ga-CAU-13-np (np stand for narrow pore) exhibits the same space group symmetry as Ga-CAU-13-lp but with changed cell parameters (P-1, a=6.7200(2), b=9.2179(3), c=9.5082(3)Å, α=107.359(2), β=102.691(3), γ=97.913(2)°) and thus a breathing of the framework is observed, which is shown to be reversible. Moreover, large molecules like p-xylene can be adsorbed into the pores, underlining the compound’s porosity. The particular nature of the breathing effect is substantially different compared with that known for Ga-MIL-53 based on the aromatic terephthalic acid.

Synthesis, characterization and theoretical studies of 5-(benzylthio)-1-cylopentyl-1H-tetrazole

In this study, 5-(benzylthio)-1-cylopentyl-1H-tetrazole (5B1C1HT) have been synthesized. Boiling points of the obtained compound have been determined and it has been characterized by FT-IR, 1H NMR, 13C-APT and LC–MS spectroscopy techniques. The FT-IR, 1H NMR and 13C-APT spectral measurements of the 5B1C1HT compound and complete assignment of the vibrational bands observed in spectra has been discussed. The spectra were interpreted with the aid of normal coordinate analysis following full structure optimization and force field calculations based on Density Functional Theory (DFT) at 6-311++G**, cc-pVDZ and cc-pVTZ basis sets. The optimized geometry with 6-311++G** basis sets were used to determine the total energy distribution, harmonic vibrational frequencies, IR intensities.

Obtaining, structural, magnetic and corrosive properties of Nd–Fe–B alloy thin films on glass

• Nd–Fe–B thin film alloys are obtained by vacuum evaporation method. • XRD, SEM/EDS and XPS were used for characterization of the thin film alloys. • Magnetic properties determined by the ponderomotive method permit calculation of the coercive force and magnetic saturation field of Nd–Fe–B thin layers. • Corrosive properties were determined in 3.5 wt% NaCl solution. • XPS analysis showed that the different electrochemical corrosion performance was associated with the ability of the thin films to form a big and continuous Nd 2 O 3 passive film, while the formation of Nd(OH) 3 lead to a decrease of the corrosion resistance. By “flash” method at the installation of vacuum evaporation the thin Nd–Fe–B layers of 100 nm ≤ d ≤ 1000 nm were obtained on glass support. The structure and microstructure of the thin Nd–Fe–B films was studied by X-ray diffraction analysis (XRD), scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS). The study of the specific magnetization temperature dependences of the Nd–Fe–B films on the glass substrate in the 80 ≤ T ≤ 800 K temperature range by ponderomotive method showed that the magnetization of the layer of d ≥ 1000 nm thickness are comparable to those for powder samples. The magnetization of film with d < 100 nm thickness at 100 K does not exceed 85 Å m 2 kg −1 . In such films the long-range structural order is destroyed. The values of the coercive force and magnetic saturation field of Nd–Fe–B thin layers are determined. The corrosion process of the thin Nd–Fe–B films magnets was studied experimentally in 3.5 wt% NaCl solution. X-ray photoelectron spectroscopy (XPS) analysis showed that the different electrochemical corrosion performance was associated with the ability of the thin films to form a big and continuous Nd 2 O 3 passive film, while the formation of Nd(OH) 3 lead to a decrease of the corrosion resistance.

Vibrational spectra and normal coordinate analysis of 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FTIR spectroscopy in the range 50–4000cm−1 and 450–4000cm−1 respectively, for 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate (2H3MPPLC) molecule. The molecular structure, fundamental vibrational frequencies and intensities of the vibrational bands were interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) and ab initio HF methods with 6-31G(d,p) basis set. The complete vibrational assignments of wave numbers were made on the basis of potential energy distribution (PED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The scaled B3LYP/6-31G(d,p) results show the best agreement with the experimental values over the other method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results confirm the occurrence of intramolecular charge-transfer (ICT) within the molecule. The dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the investigated molecule has been computed using B3LYP/6-31G(d,p) method. Mulliken population analysis on atomic charges was also calculated. Besides, frontier molecular orbitals, molecular electrostatic potential (MEP) and thermodynamic properties were performed.

Spectroscopic (FT-IR, FT-Raman, NMR and UV–Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid

The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000–400 and 4000–100cm−1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

Segregation effects on the properties of (AuAg)₁₄₇.

AuAg nanoclusters are promising supported co-catalysts for photocatalytic hydrogen reduction. However, beyond the quantum regime (N > 100) little is known about how the electronic properties of these nanoparticles are affected by chemical ordering. We investigate the effects of chemical ordering on the properties of 147-atom cuboctahedral AuAg nanoclusters, using empirical potentials coupled with an atomic-swap basin-hopping search to optimise the elemental distribution, with the lowest energy arrangements then reminimised using Density Functional Theory (DFT). Force-field calculations show Au atoms preferentially occupy sub-surface positions in the bimetallic structures, which results in the formation of a pseudo-onion structure for Ag-rich compositions. At the DFT-level, however, an Ag core surrounded by an Au shell (Ag@Au) is energetically favoured, as electron density can be drawn more readily when Au atoms are positioned on the nanocluster surface, thus resulting in a partial negative charge. Core@shell configurations are analogous to structures that can be chemically synthesised, and further detailed electronic analysis is discussed in the context of nanocluster applications to co-catalysed photocatalysis.

Experimental and theoretical (FT-IR, FT-Raman, UV–vis, NMR) spectroscopic analysis and first order hyperpolarizability studies of non-linear optical material: (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one using density functional theory

A combined experimental and theoretical investigation on FT-IR, FT-Raman, NMR, UV–vis spectra of a chalcone derivative (2E)-3-[4-(methylsulfanyl) phenyl]-1-(4-nitrophenyl) prop-2-en-1-one (4N4MSP) has been reported. 4N4MSP has two planar rings connected through conjugated double bond and it provides a necessary configuration to show non-linear optical (NLO) response. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) with B3LYP functional and 6-311++G(d,p) basis set combination. The analysis of the fundamental modes was made with the help of potential energy distribution (PED). Molecular electrostatic potential (MEP) surface was plotted over the geometry primarily for predicting sites and relative reactivities towards electrophilic and nucleophilic attack. The delocalization of electron density of various constituents of the molecule has been discussed with the aid of NBO analysis. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were calculated by time-dependent density functional theory (TD-DFT) and the results complement the experimental findings. The recorded and calculated 1H chemical shifts in gas phase and MeOD solution are gathered for reliable calculations of magnetic properties. Thermodynamic properties like heat capacity (C°p,m), entropy (S°m), enthalpy (H°m) have been calculated for the molecule at the different temperatures. Based on the finite-field approach, the non-linear optical (NLO) parameters such as dipole moment, mean polarizability, anisotropy of polarizability and first order hyperpolarizability of 4N4MSP molecule are calculated. The predicted first hyperpolarizability shows that the molecule has a reasonably good nonlinear optical (NLO) behavior.

Theoretical spectroscopic characterization at low temperatures of detectable sulfur-organic compounds: Ethyl mercaptan and dimethyl sulfide

Highly correlated ab initio methods are used for the spectroscopic characterization of ethyl mercaptan (CH3CH2 (32)SH, ETSH) and dimethyl sulfide (CH3 (32)SCH3, DMS), considering them on the vibrational ground and excited torsional states. Since both molecules show non-rigid properties, torsional energy barriers and splittings are provided. Equilibrium geometries and the corresponding rotational constants are calculated by means of a composite scheme based on CCSD(T) calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The ground and excited states rotational constants are then determined using vibrational corrections obtained from CCSD/cc-pVTZ force-field calculations, which are also employed to determine anharmonic frequencies for all vibrational modes. CCSD(T) and CCSD force fields are employed to predict quartic and sextic centrifugal-distortion constants, respectively. Equilibrium rotational constants are also calculated using CCSD(T)-F12. The full-dimensional anharmonic analysis does not predict displacements of the lowest torsional excited states due to Fermi resonances with the remaining vibrational modes. Thus, very accurate torsional transitions are calculated by solving variationally two-dimensional Hamiltonians depending on the CH3 and SH torsional coordinates of ethyl mercaptan or on the two methyl groups torsions of dimethyl-sulfide. For this purpose, vibrationally corrected potential energy surfaces are computed at the CCSD(T)/aug-cc-pVTZ level of theory. For ethyl mercaptan, calculations show large differences between the gauche (g) and trans (t) conformer spectral features. Interactions between rotating groups are responsible for the displacements of the g-bands with respect to the t-bands that cannot therefore be described with one-dimensional models. For DMS, the CCSD(T) potential energy surface has been semi-empirically adjusted to reproduce experimental data. New assignments are suggested for the methyl torsion bands of ETSH and a reassignment is proposed for the infrared bands of DMS (0 3 → 0 4 and 1 0 → 1 1). Our accurate spectroscopic data should be useful for the analysis of the microwave and far infrared spectra of ETSH and DMS recorded, at low temperatures, either in laboratory or in the interstellar medium.

Fourier type potential energy function for conformational change of selected organic functional groups

The energy changes associated with internal rotation of a functional group in a molecule depend on the topology of the chemical environment. Energies obtained from electron structure and force-field calculations have been analyzed by Fourier expansions. The findings show that rotation around bonds connecting atoms without lone pairs can be described with a one term Fourier-series. In contrast, two or three terms are needed if the connected atoms have lone pairs. The analysis inspires adoption of a simplified Fourier expansion that reproduces the data well, suggesting that Fourier-type-series with few terms are useful in describing any internal rotation analytically.

A thermodynamic adsorption/entrapment model for selenium(IV) coprecipitation with calcite

Selenium is an environmentally relevant trace element, while the radioisotope 79Se is of particular concern in the context of nuclear waste disposal safety. Oxidized selenium species are relatively soluble and show only weak adsorption at common mineral surfaces. However, a possible sorption mechanism for selenium in the geosphere is the structural incorporation of selenium(IV) (selenite, SeO32−) into calcite (CaCO3).In this study we investigate the interactions between selenite and calcite by a series of experimental and computational methods with the aim to quantify selenite incorporation into calcite at standard conditions. We further seek to describe the thermodynamics of selenite-doped calcite, and selenite coprecipitation with calcite.The structure of the incorporated species is investigated using Se K-edge EXAFS (isotropic and polarization dependent) and results are compared to density functional theory (DFT) calculations. These investigations confirm structural incorporation of selenite into calcite by the substitution of carbonate for selenite, leading to the formation of a Ca(SeO3)X(CO3)(1−X) solid solution.Coprecipitation experiments at low supersaturation indicate a linear increase of the selenite to carbonate ratio in the solid with the increase of the selenite to carbonate ratio in the contact solution. This relationship can be described under the assumption of an ideal mixing between calcite and a virtual CaSeO3 endmember, whose standard Gibbs free energy (G0(CaSeO3_exp)=−953±6kJ/mol, log10(KSP(CaSeO3_exp))=−6.7±1.0) is defined by linear extrapolation of the excess free energy from the dilute Henry’s law domain to X(CaSeO3)=1. In contrast to this experimental result, DFT and force field calculations predict the virtual bulk CaSeO3 endmember to be significantly less stable and more soluble: G0(CaSeO3 bulk)=−912±10kJ/mol and log10(KSP(CaSeO3_bulk))=0.5±1.7.To explain this discrepancy we introduce a thermodynamic adsorption/entrapment concept. This concept is based on the idea that the experimental value of −953±6kJ/mol reflects the Gibbs free energy of CaSeO3 within the surface layer, while the value obtained from atomistic calculations reflects bulk thermodynamic properties. In coprecipitation experiments performed at steady-state conditions the difference between these values is compensated by the supersaturation. Thus, if the Gibbs free energies of the bulk CaCO3 and CaSeO3 endmembers are substituted with the Gibbs free energies of the surface endmembers, the coprecipitation experiment can still be treated within the formalism of equilibrium thermodynamics. This concept leads to a number of important consequences, which can be tested both experimentally and theoretically.We show that selenite adsorption at the calcite surface and selenite coprecipitation with calcite under supersaturated conditions can be described with the same partition coefficient. This implies that the coprecipitation can be viewed as a sequence of adsorption and entrapment events. On the other hand, our aragonite recrystallization experiments show that at near equilibrium conditions the calcite growth is inhibited in the presence of selenite. Consistent with these observations, our DFT calculations show that the substitution of carbonate for selenite is energetically more favorable at the surface than inside the bulk.The whole set of the experimental and atomistic simulation results leads to the conclusion that the calcite–CaSeO3 solid solution can only grow continuously if the aqueous solution is supersaturated with respect to the bulk solid solution. Under these conditions selenite coprecipitates with calcite at a partition coefficient of D=0.02±0.01. If the solution is undersaturated with respect to the bulk solid solution, only surface ion-exchange occurs. Elevated selenite concentrations in bulk calcite therefore reflect non-equilibrium conditions.

Development of ABEEMσπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism

Hydrogen-bonding and stacking interactions play a unique role for structure and replication of DNA. When adenine in DNA is oxidized, it increases the number of hydrogen bond donor and acceptor sites, and may lead to various mutations. 8-oxo-A is the most common oxidative product of adenine. Taking high-level ab initio calculations as benchmarks, we developed the ABEEMσπ polarizable force field and investigated the charges, structures, energies and mutations of base pairs containing canonical bases and 8-oxo-A. During this process, we do a great deal of ab initio, ABEEMσπ and other force field calculations for investigation, testing and calibration. The results of this work show that the angle formed by two base planes is buckled in the oxidized base pairs, and 79 % of buckled angles are larger than 5.0°. Comparing the results of ab initio with those of ABEEMσπ, the linear correlation coefficients of the charges, dipole moments and interaction energies are 0.99, 0.96 and 0.96, respectively; the ABEEMσπ force field provides reliable information on hydrogen-bonding, stacking interactions and mutation processes. In the DNA double helix, the mutations of AT → GC, AT → TA or AT → CG would happen. Meanwhile, the active centers of nucleophilic or electrophilic reaction transfer during AT → GC, AT → TA and AT → CG mutations. The results also indicate that the performance of the ABEEMσπ polarizable force field is generally better than that of the common force fields, and its accuracy can compare with that of the MP2 method. These studies supply a solid basis for further investigations of dynamical behavior of DNA fragments including oxidized adenine by the ABEEMσπ polarizable force field.

Atomic-Level Characterization of Interfaces in LiCoO2

The powerful synergy between atomic-resolution electron microscopy and atomistic simulation techniques encompassing both first-principles and classical force-field calculations is illustrated through a study of grain boundaries, domain boundaries and surfaces of the lithium-ion secondary battery cathode material LiCoO2. Epitaxial thin films of LiCoO2 deposited on sapphire (0001) substrates are used as model samples, and results from simulation and experiment combined to characterize the structures and properties of representative interfaces.

An implicit evolution scheme for active contours and surfaces based on IIR filtering

In this work, we present an approach for implementing an implicit scheme for the numerical solution of the partial differential equation of the evolution of an active contour/surface. The proposed scheme is applicable to any variant of the traditional active contour (AC), irrespectively of the calculation of the image-based force field and it is readily applicable to explicitly parameterized active surfaces (AS). The proposed approach is formulated as an infinite impulse response (IIR) filtering of the coordinates of the contour/surface points. The poles of the filter are determined by the parameters controlling the shape of the active contour/surface. We show that the proposed IIR-based implicit evolution scheme has very low complexity. Furthermore, the proposed scheme is numerically stable, thus it allows the convergence of the AC/AS with significantly fewer iterations than the explicit evolution scheme. It also possesses the separability property along the two parameters of the AS, thus it may be applied to deformable surfaces, without the need to store and invert large sparse matrices. We implemented the proposed IIR-based implicit evolution scheme in the Vector Field Convolution (VFC) AC/AS using synthetic and clinical volumetric data. We compared the segmentation results with those of the explicit AC/AS evolution, in terms of accuracy and efficiency. Results show that the VFC AC/AS with the proposed IIR-based implicit evolution scheme achieves the same segmentation results with the explicit scheme, with considerably less computation time.

Relation between the changes in IL-6 and glucose in response to exercise test and investigation of physicochemical properties of IL-6 and its ligand binding site

Obesity is known to be associated with systemic inflammation. In this study, we investigated serum Interleukin 6 and glucose concentration (IL-6) in response to a stepwise cycling test in obese men. For this purpose, serum IL6 and glucose concentration were measured in eighteen none-trained adult obese men. Serum IL-6 increased significantly and glucose concentration decreased by exercise test when compared to pre test. Changes in IL-6 were negatively correlated with change in glucose concentration. In present study, also, the structure of protein IL-6 was selected from the protein data bank (PDB code 1ALU). We choose Monte Carlo and AMBER force fields for molecular mechanics calculations. Temperatures of calculation were kept 288-315 K. Moreover, additional parameters were calculated using the QSAR Properties Module of HyperChem 8.6 software. We measured partial derivative of each subunit in constant and variable volume and temperature. This survey results will help us find the best thermodynamics properties for IL6 and finding the best active site for activity in different state of temperature.

Studies of the molecular geometry, vibrational spectra, Frontier molecular orbital, nonlinear optical and thermodynamics properties of Aceclofenac by quantum chemical calculations

The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000–400 and 4000–100cm−1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

Polarized Matrix Infrared Spectra of Cyclopentadienone: Observations, Calculations, and Assignment for an Important Intermediate in Combustion and Biomass Pyrolysis

A detailed vibrational analysis of the infrared spectra of cyclopentadienone (C5H4═O) in rare gas matrices has been carried out. Ab initio coupled-cluster anharmonic force field calculations were used to guide the assignments. Flash pyrolysis of o-phenylene sulfite (C6H4O2SO) was used to provide a molecular beam of C5H4═O entrained in a rare gas carrier. The beam was interrogated with time-of-flight photoionization mass spectrometry (PIMS), confirming the clean, intense production of C5H4═O. Matrix isolation infrared spectroscopy coupled with 355 nm polarized UV for photoorientation and linear dichroism experiments was used to determine the symmetries of the vibrations. Cyclopentadienone has 24 fundamental vibrational modes, Γvib = 9a1 ⊕ 3a2 ⊕ 4b1 ⊕ 8b2. Using vibrational perturbation theory and a deperturbation-diagonalization method, we report assignments of the following fundamental modes (cm(-1)) in a 4 K neon matrix: the a1 modes of X̃ (1)A1 C5H4═O are found to be ν1 = 3107, ν2 = (3100, 3099), ν3 = 1735, ν5 = 1333, ν7 = 952, ν8 = 843, and ν9 = 651; the inferred a2 modes are ν10 = 933, and ν11 = 722; the b1 modes are ν13 = 932, ν14 = 822, and ν15 = 629; the b2 fundamentals are ν17 = 3143, ν18 = (3078, 3076) ν19 = (1601 or 1595), ν20 = 1283, ν21 = 1138, ν22 = 1066, ν23 = 738, and ν24 = 458. The modes ν4 and ν6 were too weak to be detected, ν12 is dipole-forbidden and its position cannot be inferred from combination and overtone bands, and ν16 is below our detection range (<400 cm(-1)). Additional features were observed and compared to anharmonic calculations, assigned as two quantum transitions, and used to assign some of the weak and infrared inactive fundamental vibrations.