Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar （HP） model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

A neural network protocol for predicting molecular bond energy

Molecular bond energy is a key parameter for analyzing the properties of chemical activity,stability and flexibility.Calculating bond energy is a challenge due to the cost of first-principles simulations and unsatisfactory prediction using empirical formula.Here we show that a neural network(NN)machine-learning method can achieve quick prediction of bond energies of organic molecules.Using atomic species and charge information as descriptors,we trained a NN protocol and applied it to predict the bond energy in a certain chemical bond that agreed with density functional theory calculations.This protocol also provided a way to evaluate the effects of different methods of atomic charge analysis on NN training.Trained to accurately estimate bond energies,this NN protocol provides a cost-effective tool for optimizing chemical reactions,accelerating molecular design,and other important applications.

Bonding Energy of a Molecular Orbital(Ⅱ)——Ab initio Calculation

Calculation of the bonding energy of a molecular orbital for a series of small molecules has been carried out by using ab initio STO-3G method. The results obtained demonstrate that the concept of the molecular orbital bonding energy is applicable for judging whether a molecular orbital is bonding, nonbonding or antibonding besides Mulliken overlap criterion.

THE CALCULATION OF THE COHESIVE ENERGY OFГPHASE IN THE TRANSITIONAL LAYER FE ZN OF HEAT GALVANIZED SHEET USED IN CARS

hethesisanalysesthevalenceelectronstructuresof phase Γin Fe Zn transitionallayerof heat galvanized sheet used in cars by applying the Empirical Electron Theory of Solids andMolecules, and calculatesthebond energy ofthe major bondsand cohesiveenergy ofcrystals,from which we draw theconclusion:sincecrystal has alargercohesiveenergy, it has higherhardness, butsinceitsbondenergyisratherlow ,itiseasytobreak under pressurefrom out side, and thecrackiseasytocome up andspreadin phase Γ.

Is HOMO Energy Level a Good Parameter to Characterize Antioxidant Activity

Semiempirical quantum chemical method AM1 was employed to calculate the highest occupied molecular orbital (HOMO) energy levels (E-HOMO) for various types of antioxidants. It was verified that the correlation between logarithm of free radical scavenging rate constants (1gks) and E-HOMO substantially arises from the correlation between E-HOMO and O-H bond dissociation energies (BDE) of antioxidants. Furthermore, E-HOMO were poorly correlated with the logarithm of relative free radical scavenging rate constants (1gk(3)/k(1)) for various types of antioxidants that possess complex structures (r = 0.5602). So in a broad sense, E-HOMO was not an appropriate parameter to characterize the free radical scavenging activity of antioxidants.

The evaluation of bond dissociation energies for NO2 scission in nitro compounds using density functional and complete basis set methods

By using the density functional theory （B3LYP） and four highly accurate complete basis set （CBS-Q, CBS-QB3, CBS-Lq, and CBS-4M）ab initio methods, the X（C, N, O）-NO2 bond dissociation energies （BDEs） for CH3NO2, C2H3NO2, C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 （CH3）2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy （BDE）; however, all four CBS models are generally able to give reliable predication of the X（C, N, O）-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered, Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.

Density Functional Calculations of C–NO_2 Bond Dissociation Energies for Nitroalkanes Molecules

Bond dissociation energies for the removal of nitrogen dioxide group in some nitroalkane energetic materials have been calculated by using the three hybrid density functional theory （DFT） methods B3LYP, B3PW91 and B3P86 with 6-31g^＊＊ and 6-311g^＊＊ basis sets. The computed BDEs have been compared with the available experimental results. It is found that the B3P86 method with 6-31g^＊＊ and 6-311g^＊＊ basis sets can obtain satisfactory bond dissociation energies （BDEs）, which are in extraordinary agreement with the experimental data. Considering the smaller mean absolute deviation and maximum difference, the reliable B3P86/6-311g^＊＊ method was recommended to compute the BDEs for the removal of nitrogen dioxide group in the nitroalkane energetic materials. Using the method, the BDEs of 8 other nitroalkane energetic materials have been calculated and the maximum difference from experimental value is 1.76 kcal.mo1^-1 （for the BDE of tC4Hg-NOz）, which further proves the reliability of B3P86/6-311g^＊＊ method. In addition, it is noted that the BDEs of C-NO2 bond change slightly for main chain nitroalkane compounds with the maximum difference of only 3.43 kcal mo1^-1.

Theoretical Study of the N-NO_2 Bond Dissociation Energies for Energetic Materials with Density Functional Theory

The N-NO2 bond dissociation energies （BDEs） for 7 energetic materials were computed by means of accurate density functional theory （B3LYP, B3PW91 and B3P86） with 6-31G＊＊ and 6-311G＊＊ basis sets. By comparing the computed energies and experimental results, we find that the B3P86/6-311G＊＊ method can give good results of BDE, which has the mean absolute deviation of 1.30kcal/mol. In addition, substituent effects were also taken into account. It is noted that the Hammett constants of substituent groups are related to the BDEs of the N-NO2 bond and the bond dissociation energies of the energetic materials studied decrease when increasing the number of NO2 group.

Quantum chemical calculations of bond dissociation energies for COOH scission and electronic structure in some acids

Quantum chemical calculations are performed to investigate the equilibrium C-COOH bond distances and the bond dissociation energies（BDEs） for 15 acids.These compounds are studied by utilizing the hybrid density functional theory（DFT）（B3LYP,B3PW91,B3P86,PBE1PBE） and the complete basis set（CBS-Q） method in conjunction with the 6311G^＊＊ basis as DFT methods have been found to have low basis sets sensitivity for small and medium molecules in our previous work.Comparisons between the computational results and the experimental values reveal that CBS-Q method,which can produce reasonable BDEs for some systems in our previous work,seems unable to predict accurate BDEs here.However,the B3P86 calculated results accord very well with the experimental values,within an average absolute error of 2.3 kcal/mol.Thus,B3P86 method is suitable for computing the reliable BDEs of C-COOH bond for carboxylic acid compounds.In addition,the energy gaps between the highest occupied molecular orbital（HOMO） and the lowest unoccupied molecular orbital（LUMO） of studied compounds are estimated,based on which the relative thermal stabilities of the studied acids are also discussed.

Bonding Energies and Structural Study of Alkylaluminium

Neutral aluminium alkyls are well known to act as ethylene oligomerization and polymerization catalysts and cocatalysts.On the basis of the full optimization of alkylaluminium compounds with Gaussian 98 program package at the B3LYP/6-31G＊＊ level,the selected structures and bonding energies were investigated extensively.The geometries and bonding energies of AlR3（R = H,CH3,C2H5,C3H7,C4H9） and Al（C2H5）2R＇（R＇ = C2H5,C3H7,C4H9,C5H11,C6H13） were investigated extensively,and we found that,along with the prolongation of carbon chains the terminal C-C bond is shortened gradually until to a constant value of about 0.1532 nm in C4H9;and the bonding energy almost remains constant.The dative bonding of C2H4 to Al（C2H5）3,whose bonding energy is only 15.30 kJ/mol,is very weak.

Covalent electron density analysis and surface energy calculation of gold with the empirical electron surface model

Based on the empirical electron surface model （EESM）,the covalent electron density of dangling bonds （CEDDB） was calculated for various crystal planes of gold,and the surface energy was calculated further.Calculation results show that CEDDB has a great influence on the surface energy of various index surfaces and the anisotropy of the surface.The calculated surface energy is in agreement with experimental and other theoretical values.The calculated surface energy of the close-packed （111） surface has the lowest surface energy,which agrees with the theoretical prediction.Also,it is found that the spatial distribution of covalent bonds has a great influence on the surface energy of various index surfaces.Therefore,CEDDB should be a suitable parameter to describe and quantify the dangling bonds and surface energy of various crystal surfaces.

Density Functional Theory Study of Marine Polybrominated Diphenyl Ethers in Anaerobic Degradation

Polybrominated diphenyl ethers(PBDEs)are a kind of serious pollutants in the ocean.Biodegradation is considered as an economical and safe way for PBDEs removal and reductive debromination dominates the initial pathway of anaerobic degradation.On the basis of experimental study,Octa-BDE 197,Hepta-BDE 183,Hexa-BDE 153,Penta-BDE 99 and Tetra-BDE 47 were selected as the initial degradation objects,and their debromination degradation were studied using density functional theory.The structures were optimized by Gaussian 09 program.Furthermore,the molecular orbitals and charge distribution were analyzed.All C-Br bond dissociation energies at different positions including ortho,meta and para bromine atoms were calculated and the sequence of debromination was obtained.There is a close relationship between molecular structure,charge,molecular orbital and C-Br bond.All PBDEs exhibited similar debromination pathways with preferential removal of meta and para bromines.

Effects of Bases on the Stabilities of Nucleoside C4'Radicals

C4'-H bond dissociation enthalpies of nucleosides were predicted using theoretical methods to a precision of 1-2 Kcal/mol. It was found that the stability of the C4' nucleoside radical is slightly dependent on the base. The orders of stability are dA < dG < dT < dC for deoxynucleosides and U < G < A = C for nucleosides.

Analytical Approach to Clusters in near Critical CO2

Clusters greatly influence thermophysical properties of near critical gases. The cluster structures of supercritical fluids in general and Carbon Dioxide especially are important for the advanced supercritical fluid technologies and analytics development. The paper extends to near critical densities the developed earlier methods to extract the clusters’ properties from Online Electronic Database of NIST on thermophysical properties of fluids. This Database contains a hidden knowledge of cluster fractions’ properties in real gases. The discovered earlier linear chain clusters dominate at intermediate densities. Their properties can be extrapolated to high density gases, thus opening the way to study large 3D clusters in near critical zone. The potential energy density of a gas, cleared from the chain clusters’ contribution, reflects only the 3D clusters’ characteristics. A series expansion of this value by the Monomer Fraction density discovers properties of n-particle 3D clusters. The paper demonstrates a discrete row of 3D clusters’ particle numbers and gives estimations for bond energies of these clusters.

Theoretical Insights into the Inhibition Performance of Three Neonicotine Derivatives as Novel Type of Inhibitors on Carbon Steel

The adsorption process of new nicotinic derivatives on Fe(110)surface and diffusion of corrosive particles in inhibition film were studied by quantum chemistry and molecular dynamics simulation,and inhibition mechanism of inhibitor was discussed.The results indicated that the main active sites of three inhibitors are located in N atoms on the five membered ring.The inhibitor YM-1 has the strongest activity of electrophilic reaction,and the adsorption process of inhibitor molecules is polycentric chemisorption.The adsorption energy for inhibitors followed the order of YM-1>YM-2>YM-3.The adsorption film YM-1 more effectively impedes the diffusion and migration of the corrosive particles,and also has the best inhibitory effect on Cl-.In addition,the bond energy of chemical bond formed between inhibitor and Fe atom increases as the increase of temperature.The interaction between corrosive particles and inhibitors is dominated by Van der Waals force.

Aromatic Character of All Possible C_(36)H_2 Isomers

The stability of C36H2 isomers and selection rules for choosing position in addition reactions based on symmetrical C36（D6h and D2d） fullerene have been studied by means of Aihara＇s topological resonance energy （TRE） and bond resonance energy （BRE） methods. The relation between the addition pattern and BREs is established, showing high antiaromatic bonds are preferred for addition. These results show that TRE and BRE methods can be used to predict and interpret addition sites for these systems.

Relativistic density functional investigation of UX_6(X=F,Cl,Br and I)

The molecular structures and the vibrational frequencies of uranium hexahalides UX6 （X=F, Cl, Br and I） molecules are investigated by using local density approximation （LDA） and generalised gradient approximation （GGA） functions （BP, BLYP and RPBE） in combination with two different relativistic methods （scalar and scalar＋spin-orbit relativistic effects）. The calculated results show that the differences are trivial between scalar and scalar＋spin-orbit relativistic methods. The vibrational frequencies are also compared with existing experimental values, and overall, the RPBE approach gives the smallest error. The bond dissociation energies （BDEs） of UX6 are computed by using the RPBE function, thereby obtaining exact vibrational frequencies. In addition, the calculated magnitudes of the spin orbit effect on the BDE of UX6 （X=F, Cl, Br, and I） are found to be approximately -0.3198, 0.3218, -0.3609 and -0.4415 eV, respectively.

DFT Study on the Antioxidant Activity of a Modeled p-Terphenyl Derivative

Relationships between the structure characteristics of natural p-terphenyl com- pounds isolated from three edible mushrooms （Thelephora ganbajun, Thelephora aeronautical, and Boletopsis grisea） indigenous to China and their mechanism of antioxidant activity were studied. Geometry structures of terphenyl molecule and four corresponding radicals, bond dissociation energy （BDE）, frontier orbitals （HOMO and LUMO） and single electron density were calculated using DFT methods （B3LYP/6-311G＊＊）. The computational results which are consistent with the experimental data well show that terphenyl molecule scavenges DPPH radical by hydrogen abstract mechanism and the high antioxidant activity depends on the substitution position of hydroxyls. Two active 7-, 8-hydroxyls facilitate the hydrogen abstraction due to the intramolecular hydrogen bond and the resonance effect makes 4-hydroxyl radical more stable.

Extraction Difficulty of Lithium Ions from Various Crystal Planes of Lithium Titanate

To study the extraction difficulty of lithium ions from various crystal planes of Li2 TiO3, according to the first principle, four representative crystal surfaces of Li2TiO3（precursor）,（-133）,（-206）,（002） and（-131）, were selected to establish a model and to calculate the surface energy, bond length and population using Materials Studio 5.5（MS 5.5）. The results demonstrate that there is no direct relationship between the surface energy and the order of disappearance of the four diffraction peaks when lithium titanate is treated with hydrochloric acid, instead, the difficulty of Li~＋ extraction from various crystal faces corresponds to the Li-O bond strength. Lithium ion is easy to remove from（-133） and（-206） due to the relatively weak Li-O bond strength. In contrast, Li＋ extraction requires a longer time for（002） and（-131）.