Modeling Metal Binding Sites in Proteins by Quantum Chemical Calculations

Modeling Metal Binding Sites in Proteins by Quantum Chemical

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

Quantum Chemical Calculations of the Structure,Property and Stability of Penta-coordinated Carbonium Ions Derived from Normal Butane

The structure and energy of the carbonium ions formed upon protonation of butane were studied by the DFT methods. Four stable structures are identified for the protonated form of n-butane, the energy increases in the following order： C2HC3〈C1HC2〈C2HH〈C1HH, and the stability decreases in the following order C2HC3〉C1HC2〉C2HH〉C1HH. The stability of the penta-coordinated carbonium ions may be explained by the electron distribution in the three-center-two-electron bonds. The delocalization of the penta-coordinated carbonium ion CHC with three-center-two-electron bonds on positive charges was stronger than that of the penta-coordinated earbonium ion CHH with three-center-two-electron bonds and its stability was higher than that of the penta-coordinated carbonium ion CHH with three-center-two-electron bonds.

Calculations of Chemical Reaction Dynamics for D+ H_2(j_i,ν_i=0)→DH(j_f, ν_f=0) + H

The constant Centrifugal potential approximation is Corrected so as to apply to the reactions of rotational excited reactants for D + H2 (j,, νi = 0 ) -DH(jf, νf = 0) + H. Our results show that the contributions from ji≠0 and Ωi terms are not negligible.

QUANTUM CHEMICAL CALCULATIONS ON THE ELECTRONIC STRUCTURE AND SPECTRA OF[Mo_3O_4-nSn]^(4+)(n=O-4)CLUSTER CATIONS

The electronic structure and spectra of [Mo3O4-nSn]^(4+)(n=0-4) cations were calculated by means of INDO/CI quantum chemistry method to account for the experimental data of their spectra in water solutions.

A review on nitrogen transformation and conversion during coal pyrolysis and combustion based on quantum chemical calculation and experimental study

The emission of NOx during coal combustion contributes to the formation of acid rain and photochemical smog,which would seriously affect the quality of atmospheric environment.Therefore,the decrease of NOx is of great importance for improving the efficient utilization of coal.The present review comprehensively summarized the influence factors and mechanisms of migration and transformation of nitrogen during the coal pyrolysis and combustion based on experimental study and quantum chemical calculation.Firstly,in the process of pyrolysis:the occurrence state and transformation of nitrogen were concluded.The influence of temperature,atmosphere,heating rate and catalyst on formation of NOx precursor and nitrogen migration path at the molecular level were summarized;Secondly,during the process of combustion:the influence of temperature,ambient oxygen concentration,physical structure of coal char,catalyst on heterogeneous oxidation of char(N)were summarized;The effects of char surface properties,catalyst and ambient atmosphere on heterogeneous reduction of NOx were also concluded.Based on the quantum chemical calculation,the reaction path of heterogeneous oxidation of char-N and heterogeneous reduction of NOx were described in detail.Current studies focus more on the generation of HCN and NH3,but in order to reduce the pollution of NOx from the source,it is necessary to further improve the process conditions and the optimal formula of producing more N2 during pyrolysis,as well as clarify the path of the generation of N2.Experiments study and quantum chemistry calculation should be combined to complete the research of directional nitrogen reduction during pyrolysis and denitration during combustion.

Hydrothermal Synthesis,Crystal Structure,Spectrum Properties and Quantum Chemical Calculation of a Trinuclear Copper(Ⅱ) Complex with 3-(Pyridin-2-yl)-1,2,4-triazole

A three-dimensional framework copper（Ⅱ） coordination polymer with copper carbonate basic and 3-（pyridin-2-yl）-1,2,4-triazole （Hpt） has been hydrothemally synthesized.The complex （2,C14 H10 CuN8 ·3H2 O） crystallizes in tetragonal,space group P4 2 /n,a=2.08581（12）,b=2.08581（12）,c=0.72331（4） nm,M r=761.73,V=3.1468（3） nm 3,Dc=1.608 g/cm 3,Z=4,F（000）=1552,GOOF=1.07,R=0.0515 and wR=0.1689.Every asymmetric unit molecular structure of the complex is composed with one copper ion,one and half water molecules and two Hpt molecules.Each copper ion is coordinated with five nitrogen atoms from four Hpt molecules,forming a distorted square pyramidal geometry.The fluorescence spectrum analysis shows that the title complex at room temperature exhibits intense photoluminescence with maximum emission at 450 nm.The quantum chemistry calculation study on the complex has been performed.The stability,some frontier molecular orbital energies and composition characteristics of some frontier molecular orbitals of the complex have been investigated.

First principles calculation on electronic structure,chemical bonding,elastic and optical properties of novel tungsten triboride

The electronic structures,chemical bonding,elastic and optical properties of the novel hP24 phase WB3 were investigated by using density-functional theory(DFT) within generalized gradient approximation(GGA).The calculated energy band structures show that the hP24 phase WB3 is metallic material.The density of state(DOS) and the partial density of state(PDOS) calculations show that the DOS near the Fermi level is mainly from the W 5d and B 2p states.Population analysis suggests that the chemical bonding in hP24-WB3 has predominantly covalent characteristics with mixed covalent-ionic characteristics.Basic physical properties,such as lattice constant,bulk modulus,shear modulus and elastic constants Cij were calculated.The elastic modulus E and Poisson ratio υ were also predicted.The results show that hP24-WB3 phase is mechanically stable and behaves in a brittle manner.Detailed analysis of all optical functions reveals that WB3 is a better dielectric material,and reflectivity spectra show that WB3 can be promised as good coating material in the energy regions of 8.5-11.4 eV and 14.5-15.5 eV.

Production calculation of the second and tertiary recovery combination reservoirs under chemical flooding

Based on the analysis of the production composition of reservoirs developed by the second&tertiary recovery combination(STRC),the relationship between the overall output of the STRC project and the production level during the blank water flooding stage is proposed.According to the basic principle of reservoir engineering that the“recovery factor is equal to sweeping coefficient multiplied by oil displacement efficiency”,the formula for calculating the ultimate oil recovery factor of chemical combination flooding reservoir was established.By dividing the reservoir into a series of grids according to differen-tial calculus thinking,the relationship between the ultimate recovery factor of a certain number of grids and the recovery de-gree of the reservoir was established,and then the variation law of oil production rate of the STRC reservoir was obtained.The concept of“oil rate enlargement factor of chemical combination flooding”was defined,and a production calculation method of reservoir developed by STRC was put forward based on practical oilfield development experience.The study shows that the oil production enhancing effect of STRC increases evenly with the in crease of the ratio of STRC displacement efficiency to water displacement efficiency,and increases rapidly with the increase of the ratio of recovery degree at flooding mode conversion to the water displacement efficiency.STRC is more effective in increasing oil production of reservoir with high recovery degree.Through practical tests of the alkali free binary flooding(polymer/surfactant)projects,the relative error of the oil production calculation method of STRC reservoir is about±10%,which meets the requirements of reservoir engineering.

Synthesis,Crystal Structure and Quantum Chemical Investigation of Bis-Schiff Base Compounds Derived from2-phenyl-1,2,3-triazole-4-carboxaldehyde with Diamine

Two new schiff base N,N＇-bis（（2-phenyl-2H-1,2,3-triazol-4-yl）methylene）-1,3-propanediamine （1） and N,N＇-bis（（2-phenyl-2H-1,2,3-triazol-4-yl）methylene） -1,4-butanediamine （2） were synthesized by condensation of 2-phenyl-1,2,3-triazole-4-carboxaldehyde with diamine, and characterized by elemental analysis, IR, IH NMR and MS spectra. Their crystal structures were determined by X-ray single crystal diffraction. Both crystals belong to the monoclinic system, space group P21/c. For compound 1（C21H20N8, Mr=384.45）： a = 16.314（3）, b =5.7168（11）, c = 21.316（4） A, β = 105.3（2）°, Z = 4, V = 1917.6（7） A^3, De =1.332 g/cm^3, F（000） = 808,μ = 0.086 mm 1, R = 0.0533 and wR = 0.1460; for compound 2 （C22H22N8, Mr=398.48）： a = 8.6156（17）, b = 5.2964（11）, c = 22.665（5）A, β = 100.54（3）°, Z = 2, V = 1016.8（4） A^3, De= 1.302 g/cm^3, F （000） = 420, μ = 0.083 mm^-1, R = 0.0373 and wR = 0.1155. Based on the crystal data, quantum chemistry calculation was performed on the two title compounds by means of Gaussian 98 program. The molecular orbital energies and atomic net charges population were obtained. Furthermore, we antilyzed their active atoms. The investigation can serve as a theoretical guide to study the synthesis and activity of the title compounds.

Quantum Chemistry Calculations on the Interaction Between Kaolinite and Gold

The density,function and discrete variation method (DFT - DVM) is used to study the interaction between kaolinite and gold. The correlation among the structure, chemical bond and stability is discussed. Several models are selected without gold and with gold in different directions and sites. The results show that the models with gold on the edge of kaolinite basal layer are more stable than those with gold above or under the layer, the models with gold near to [AlO2 (OH)(4)] octahedra are more stable than those with gold near to the vacancy without aluminium. The interaction between gold and the surface ions of kaolinite is strong enough to form the surface complexes.

Electronic Structure and Chemical Bond of Titanium Diboride

Titanium diboride was calculated by the density function and discrete variational (DFT-DVM) method to study the relation between structure and properties.Titanium and its first-nearest boron atoms form a strong covalent bond,so TiB 2 has high melting point,hardness and chemical stability.Titanium atom releases two electrons to form Ti 2+ ions,and a boron atom gets one electron to come into B- ion.B- takes the sp2 hybrid and forms σ bonds to link other boron atoms in the same layer.The other one 2p z orbital of every B- ion in the same layer interacts each other to form the π molecular orbital,so TiB 2 has fine electrical property.The calculated density of state is close to the result of XPS experiment of TiB 2.Mainly Ti3d and B2p atomic orbitals contribute the total DOS near the Fermi level.

Synthesis, Crystal Structure,Characterization and Quantum Chemical Studies on 1N-Acetyl-3-(2,4-dichloro-5-fluoro- phenyl)-5-(p-methyl-phenyl)-2-pyrazoline

1N-Acetyl-3-（2,4-dichloro-5-fluoro-phenyl）-5-（p-methyl-phenyl）-2-pyrazoline has been synthesized and characterized by elemental analysis, IR, UV-Vis and X-ray single-crystal diffraction. Ab intio calculations have been carded out for the compound by using both B3LYP and HF methods at the 6-31G^＊ basis set. The calculated results show that the predicted geometry can well reproduce the structural parameters. The electronic absorption spectra calculated by B3LYP/6-31G^＊ method are approximate to the experiments and the Natural Bond Orbital （NBO） analyses suggest that the above electronic transitions are mainly assigned to n→π^＊ and π→π^＊ transitions. CIS-HF/6-31G^＊ method is not suitable to predict the electronic spectra for the title compound. The calculation of the second order optical nonlinearity was carded out, giving the value of molecular hyperpolarizability equal to 2.194^＋ 10^-30 esu. On the basis of vibrational analyses, the thermodynamic properties of the compound at different temperature have been calculated, revealing the correlation between C p, m^0, S m^0, H m^0 and temperature.

Chemical Degradation of Indigo Potassium Tetrasulfonate Dye by Advanced Oxidation Processes

The experimental degradation of a water soluble dye, potassium indigo tetrasulfonate salt, has been studied using stand-alone ozonation and photocatalytic oxidation process. Progress of the dye oxidation was followed by UV-VIS spectrophotometric measurements at controlled operating conditions. The organic content of reaction samples was measured to verify the process efficiency in dye mineralization. According to current results, almost complete color removal was obtained for ozonation within about 1 h reaction time. The reduction of the organic load was almost 80% from its original while initial sulphur content decreased to 32.5%. Dye conversion of 100% was obtained by means of a photocatalytic process using TiO2 as catalyst at 294 nm irradiated UV light. This complete color removal for the catalytic process was observed within 7 min of reaction time. The calculated initial rate of reaction of photocatalysis treatment was 8 times faster than that of ozonolysis. However, the remaining organic load of photocatalysis was almost 88% from its original while the final sulphur content was 27.3%. This contrasting behavior of the performance of the type of oxidation process stressed importance of physicochemical phenomena and intermediates molecules present during dye degradation. An insightful and mechanistic aspect of the dye oxidation was developed by performing quantumchemical calculations.

Structural Evolution and Electronic Properties of Au2Gen-/0（n=1-8） Clusters: Anion Photoelectron Spectroscopy and Theoretical Calculations

Investigating the structures and properties of Au-Ge mixed clusters can give insight into the microscopic mechanisms in gold-catalyzed Ge films and can also provide valuable information for the production of germanium-based functional materials. In this work, size-selected anion photoelectron spectroscopy and theoretical calculations were used to explore the structural evolution and electronic properties of Au2Gen^-/0 (n=1-8) clusters. It is found that the two Au atoms in Au2Gen^-/0 (n=1-8) showed high coordination numbers and weak aurophilic interactions. The global minima of Au2Gen- anions and Au2Gen neutrals are in spin doublet and singlet states, respectively. Au2Gen- anions and Au2Gen neutrals showed similar structural features, except for Au2Ge4^-/0 and Au2Ge5^-/0. The C2v symmetric V-shaped structure is observed for Au2Ge1^-/0, while Au2Ge2^-/0 has a C2v symmetric dibridged structure. Au2Ge3^-/0 can be viewed as the two Au atoms attached to different Ge-Ge bonds of Ge3 triangle. Au2Ge4- has two Au atoms edge-capping Ge4 tetrahedron, while Au2Ge4 neutral adopts a C2v symmetric double Au atoms face-capping Ge4 rhombus. Au2Ge5-8^-/0 show triangular, tetragonal, and pentagonal prism-based geometries. Au2Ge6 adopts a C2v symmetric tetragonal prism structure and exhibits σ plus π double bonding characters.

Synthesis, Structure and Quantum Mechanical Calculations of Methyl 2-(5-((Quinolin-8-yloxy)-methyl)-1,3,4-oxadiazol-2-ylthio)-acetate

The title compound was synthesized by the base catalyzed reaction of 5-（（quinolin- 8-yloxy）methyl）-1,3,4-oxadiazole-2（3H）-thione with methyl chloroacetate. The structure was supported by the spectroscopic data and unambiguously confirmed by single-crystal X-ray diffraction studies. It crystallizes from a methanol solution in the triclinic space group Pi with unit cell dimensions a = 7.4509（9）, b = 10.2389（12）, c = 12.2299（15）A, a = 74.771（2）, β = 77.956（2）, 7 = 69.263（2）°, V = 834.98（17） A3 and Z = 2. In order to gain some valuable insights into the molecular structure, the quantum mechanical calculations were performed using both HF and time-dependent density functional theory at the B3LYP/6-31G（d,p） level. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock （HF） and density functional theory （DFT） with the 6-31G（d） basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound was examined using the B3LYP method with the 6-31G（d） basis set. The harmonic vibrational frequencies calculated have been compared with the experimental FTIR and FT-Raman spectra. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance （NMR） calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of the title compound. Moreover, molecular electrostatic potential and thermodynamic parameters of the title compound were investigated by theoretical calculations.

CCSD(T) study on the structures and chemical bonds of AnO molecules (An = Bk–Lr)

The molecular geometries and dissociation energies of AnO (An = Bk–Lr) molecules were first obtained at thecoupled-cluster single-, double-, and perturbative triple-excitations [CCSD(T)] level of theory. Four hybrid functionals,B3LYP, M06-2X, TPSSh, and PBE0, were also employed in the calculations for the sake of comparison. In comparison ofthe CCSD(T) results, B3LYP, TPSSh, and PBE0 functionals can obtain more appropriate results than M06-2X and MP2.The analyses on molecular orbitals show that the 7s, 6d, and 5f atomic orbitals of actinide (An) atoms participate in thebonding of An–O bonds. The partial covalent nature between An and O atoms is revealed by QTAIM analyses.

Quantum chemical aided molecular design of ionic liquids as green electrolytes for electrodeposition of active metals

Quantum chemical calculation was used to estimate the reduction potentials of 25 organic cations and the oxidation potentials of 11 anions.This information was used to select promising cations and anions for the preparation of ionic liquids as green electrolytes for electrodeposition of active metals.The reasonable linear correlations between the lowest unoccupied molecular orbital(LUMO)energies and the reduction potentials of cations,and the linear relationships between the oxidation potentials and the highest occupied molecular orbital(HOMO)energies of anions were obtained.The orders of electrochemical stability for cations and anions being obtained agree well with the experimental measurements.The suitable ionic liquids with sufficiently wide electrochemical windows for electrodeposition of active metals are suggested to be[Emim]NTf2,[Bmim]NTf2,[Bmim]BF4, [Bmim]PF6,[Bmim]CTf3,[Emim]BF4,[Emim]PF6,[Emim]CTf3..

Synthesis, Spectroscopic Investigations, Quantum Chemical Studies (<i>Ab-initio</i>&DFT) and Antimicrobial Activities of 3-(3-Chloro-4,5-dimethoxy-phenyl)-1-(4, 5-dimethoxy-2-methyl-Phenyl) prop-2-en-1-one

The chalcones (1,3-diaryl-2-propenones) and their derivatives are important intermediates in organic synthesis and have widespread applications in medicinal industry. The title choloro chalcone derivative, 3-(3-chloro-4,5-dimethoxyphenyl)-1-(4,5-dimethoxy-2-methyl phenyl) prop-2-en-1-one, has been synthesized. It is characterized by FTIR, 1H NMR, 13C NMR and single crystal X-ray diffraction. Title compound crystallizes in monoclinic space group C2/c with a = 23.540(11) ?, b = 9.738(4) ?, c = 17.305(7) ?, β = 106.37 (3)°, V = 3806(3) ?3 and Z = 8. The mean plane of the two substituted benzene rings are twisted by 66.29 (12)° with respect to each other. Ab-initio and density functional Theory (DFT) calculations have been carried out for the title molecule using RHF/6-311G and B3LYP/6-311G basis set respectively. The calculated results show that the predicted geometry can well reproduce structural parameters. In addition, frontier molecular orbitals and Mullikan charge distributions are carried out by using RHF and B3LYP methods. The calculated HOMO and LUMO energies show that charge transfer occurs in the molecule. Numbers of weak but significant interactions like C-H···O, C-H···π and π-π are involved in the stability of the structure. The weak π-π stacked interaction involves the centroids of the methyl phenyl rings with Cg-Cg separation distance of 3.857(2) ?. Synthesized compound has been screened for its antimicrobial activity against different panels of organisms.