Electronic structure and spectroscopic properties of 6‐aminophenanthridine and its derivatives: Insights from density functional theory

6‐Aminophenanthridine (6AP) and its derivatives show important biological activities as antiprion compounds and inhibitors of the protein folding activity of the ribosome. Both of these activities depend on the RNA binding property of these compounds, which has been recently characterized by fluorescence spectroscopy. Hence, fundamental insights into the photophysical properties of 6AP compounds are highly important to understand their biological activities. In this work, we have calculated electronic structures and optical properties of 6AP and its three derivatives 6AP8CF₃, 6AP8Cl, and 6APi by density functional theory (DFT) and time‐dependent density functional theory (TDDFT). Our calculated spectra show a good agreement with the experimental absorption and fluorescence spectra, and thus, provide deep insights into the optical properties of the compounds. Furthermore, comparing the results obtained with four different hybrid functionals, we demonstrate that the accuracy of the functionals varies in the order B3LYP > PBE0 > M062X > M06HF. © 2015 Wiley Periodicals, Inc.     

Oxidation potential of thiophene oligomers: Theoretical and experimental approach

Intrinsic properties of conducting polymers, such as oxidation potential and band gap, are very important for designing new materials with improved properties. Computational chemistry offers suitable tools capable of predicting these quantities. This work presents electrochemical information about accurate oxidation potentials of oligothiophenes and polymer band gap. These are compared to theoretical predictions based on electronic structure calculations at Density Functional Theory levels, coupled with self‐consistent reaction field. All computational protocols gave a qualitative prediction of the experimental trend. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2011     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.     

聚合位点对齐聚乙烯基噻吩光谱的影响

利用密度泛函理论PBE0方法,在6-31G基组水平上,对12种采用不同聚合位点的乙烯基噻吩二聚体分子进行了全优化,得到分子的紫外-可见吸收光谱.探讨了聚合位点对齐聚乙烯基噻吩吸收光谱、电子亲和势、电离能和重组能的影响,并研究了聚合度对乙烯基噻吩齐聚物吸收光谱的影响.计算结果表明:采用邻位聚合的乙烯基噻吩二聚体的能隙最小,电离能EIP最小,电子亲和势EEA最高,最大吸收波长较大,吸收强度大,λmax=377.33nm,f=1.0242.随着聚合度的增加,齐聚乙烯基噻吩的吸收光谱发生红移,吸收峰变宽,吸光度增大.十六聚体的最大吸收范围为500~1200nm,最大吸收波长为801.28nm时吸收值为7.003×105L·mol~(-1)·cm~(-1).     

左旋葡聚糖热解机理的密度泛函理论研究

采用密度泛函理论B3LYP/6-31++G(d,p)方法,对纤维素热解的主要产物左旋葡聚糖的热解反应机理进行了理论计算分析,设计了四种可能的热解反应途径, 对各种反应的反应物、产物和过渡态的结构进行了能量梯度全优化。计算结果表明,左旋葡聚糖开环成链状中间体时,首先,左旋葡聚糖中的两个半缩醛键C(1)-O(7)和C(6)-O(8)断裂,经过渡态TS₁形成中间体IM₁,同时,C(6)-O(7)结合成键使C(5)-C(6)-O(7)形成环状结构,该反应的能垒较高,为296.53 kJ/mol,然后IM₁经过渡态TS₂转变为中间体IM₂,该反应的能垒为234.09 kJ/mol;对IM₂设计了四条可能的反应路径,反应路径2和3能垒较低,是IM₂最可能的热解反应途径;在反应路径1和4中都包含了脱羰基反应,其反应能垒较高,不易发生。     

Actinium coordination chemistry: A density functional theory study with monodentate and bidentate ligands

In the current study, the coordination chemistry of nine-coordinate Ac(III) complexes with 35 monodentate and bidentate ligands was investigated using density functional theory (DFT) in terms of their geometries, charges, reaction energies, and bonding interactions. The energy decomposition analysis with naturals orbitals for chemical valence (EDA-NOCV) and the quantum theory of atoms in molecules (QTAIM) were employed as analysis methods. Trivalent Ac exhibits the highest affinities toward hard acids (such as charged oxophilic donors, fluoride), so its classification as a hard acid is justified. Natural population analysis quantified the involvement of 5f orbitals on Ac to be about 30% of total valence electron natural configuration indicating that Ac is a member of the actinide series. Pearson correlation coefficients were used to study the pairwise correlations among the bond lengths, ΔG reaction energies, charges on Ac and donor atoms, and data from EDA-NOCV and QTAIM. Strong correlations and anticorrelations were found between Voronoi charges on donor atoms with ΔG, EDA-NOCV interaction energies and QTAIM bond critical point densities.     

Assessing the performance of density functional theory for the dynamic polarizabilities of amino acids: Treatment of correlation and role of exact exchange

The theoretical determination of electric response properties of the biological systems is a field where the application of density functional theory (DFT) appears to be quite promising. In this work, the performance of 41 density functional methods is evaluated in predicting dynamic polarizabilities of an experimental benchmark set of 20 proteinogenic amino acids. The behavior of a large number of density functionals, including various types of the local spin density approximation (LSDA), generalized gradient approximation (GGA), meta‐GGA (m‐GGA), hybrid‐GGA (h‐GGA), hybrid meta‐GGA (hm‐GGA), and range‐separated hybrid‐GGA (rsh‐GGA), has been assessed for the purpose. Analyzing the results of our DFT benchmarking, we found that these computationally economical methods show very diverse predictive capability and a careful selection of DFT functionals is very important in the polarizability calculations. Considering the role of exchange, correlation, dispersion and long‐range corrections, it turned out that in the LSDA class, SVWN3 gives better results than SPL and SVWN5 toward the reference values. Of the GGA methods, OPBE outperforms all other functionals. The M06‐L is the best method of m‐GGA class. The B3LYP and TPSSh are the best functionals of h‐GGA and hm‐GGA lineages, respectively. Finally, CAM‐B3LYP is the best method of rsh‐GGA functionals that predicts the most accurate polarizability for amino acids by a large margin with respect to others. Overall, the best performing functionals turn out to be hm‐GGAs TPSSh, TPSS1KCIS, M05, tau‐HCTHhyb, and h‐GGA B3LYP. Hopefully, the results of this investigation might provide the useful guidance to propose a new exchange‐correlation functional for calculating the optical properties of biomolecular materials. © 2013 Wiley Periodicals, Inc.     

Calculation of the electronic and optical properties of indium tin oxide by density functional theory

Density functional theory (DFT) was used to calculate the bulk electronic and optical properties of indium tin oxide (ITO). The ITO model was constructed replacing indium atoms with tin atoms in the cubic unit cell of indium oxide. To allow more possibilities for tin atom substitution than afforded by the forty-atom primitive cell of indium oxide all eighty atoms of the unit cell were included in the stoichiometry (In_32−xSn_xO₄₈) using periodic boundary conditions. A number of properties of ITO were calculated including the optical band gap, charge carrier density and plasma frequency. The dependence of the electronic and optical properties of ITO on a variety of parameters such as the tin content, cubic lattice parameter and the distance between adjacent tin atoms was investigated. The electronic and optical properties agreed well with experimental data and allowed insight into the origin of the electronic and optical properties of ITO.     

Pathways of liquefied petroleum gas pyrolysis in hydrogen plasma: A density functional theory study

A density functional theory (DFT) study has been conducted in this work to investigate the pyrolysis pathways of propane and n-butane, which are the main components of liquefied petroleum gas (LPG), for better understanding the pyrolysis behavior of LPG in hydrogen thermal plasma. Over 60 possible reactions are considered. The reaction enthalpies and activation energies of these reactions are calculated and analyzed with a Gaussian method of B3LYP and basic set of 6-31G (d,p). A most possible reaction pathway is brought up. According to this reaction pathway, the main products of LPG pyrolysis are acetylene, ethylene, methane, ethane and extra hydrogen. Acetylene mainly comes from the pyrolysis of propylene and ethylene, and hydrogen abstraction reactions are the main source of extra hydrogen gas. Active H· radicals are found to play a very important role in many reactions, and they can remarkably lower the energies needed for reactions.     

Effects of hydroxyl group on H2 dissociation on graphene: A density functional theory study

Graphene-based materials are promising for hydrogen production and storage. In this work, using density functional theory calculations, we explored how a hydroxyl group influences H₂ dissociation on graphene. Presence of the hydroxyl group makes the binding of H atom with graphene stronger, as the binding energy of H atom with the hydroxyl-modified graphene is higher than that with the pristine graphene. The para-site is the most favorable site for H₂ dissociation on both the pristine and hydroxyl-modified graphene. The energy barrier of H₂ dissociation at para-site on the pristine graphene is 3.10 eV whereas that on the hydroxyl-modified graphene is 2.46 eV, indicating a more facile H₂ dissociation on the hydroxyl-modified graphene.     

Effect of trimethylsilyl substitution on the structure and properties of phthalocyanine: A density functional theory study

The geometries of four isomers of the trimethylsilyl substituted phthalocyanine (Pc)— I , II , III , and IV —have been optimized at the B3LYP/3‐21G level of density functional theory. Normal‐mode vibrational analyses have been performed and their standard thermodynamic functions, molar fractions, and electronic absorption spectra calculated. Single‐point energies have been calculated at the B3LYP/6‐311G* level for all isomers to evaluate the heats of formation from an isodesmic reaction. It is found that substitution has little influence on the geometry and electronic structures of the Pc framework. The corresponding geometric parameters in various isomers are close. According to the B3LYP/6‐311G*//B3LYP/3‐21G results, substitution at the peripheral position of the isoindole with an inner hydrogen is most favorable. The energies increase in the order of IV < II < III < I , and the energy difference between IV and I is 5.75 kJ/mol. The molar fractions of IV , II , III , and I are 0.80, 0.17, 0.02, and 0.02 and the heats of formation are 2009.96, 2010.10, 2015.85, and 2016.52 kJ/mol, respectively. This indicates that nonperipheral substituted Pcs have higher energy and little production because they are not stable under the considered conditions. The electronic spectra of the substituted Pcs calculated using the ZINDO method have two strong Q absorption bands around 700 nm and one B band around 300 nm that are slightly shifted compared with those in Pc. The ratios of the oscillator strength of the B band to the Q bands are much lowered by trimethylsilyl substitution. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

椅型碳纳米管吸附氧原子的密度泛函理论研究

利用密度泛函B3LYP对有限长扶手椅形单壁碳纳米管(3,3),(4,4)和(5,5)吸附O原子的几何结构、电子属性、反应能和红外光谱进行了系统地理论研究,获得了一些有意义的结果,主要包括如下4个方面:(1)2个O原子吸附在管外壁垂直于管轴的C—C键形成开环的轮烯结构,吸附在管内壁形成环氧结构;(2)O原子吸附在管外壁要比吸附在管内壁具有较大的能隙和吸附反应能;(3)与单壁碳纳米管管外壁吸附1个O原子相比,2个O原子吸附在管外壁具有较大的吸附反应能;(4)B3LYP得到的C—O伸缩振动频率与实验一致.     

Mechanical properties of diboron-porphyrin sheet under strain: A density functional theory study

The mechanical properties of a new two-dimensional semiconductor material named diboron-porphyrin (DP) are studied based on density functional theory. The behavior of DP monolayer under uniaxial and biaxial loadings as well as shear stress is investigated. The in-plane stiffness, Poisson's ratio, bulk and shear moduli of the DP monolayer are found to be close to those of a graphene sheet. It can be concluded that the DP monolayer has stiffness close to the graphene sheet. The difference in magnitude of in-plane stiffness and Poisson's ratio along x- and y-directions shows slightly anisotropic mechanical properties of DP monolayer. It is also observed that DP monolayers can bear high tensile strains before failure. The high stability and hardly deformable structure of DP monolayer are due to its high planar packing density which is comparable with graphene sheet. The fantastic mechanical properties of DP show these materials are desirable for application in nanomechanical devices.     

Formation mechanism of methane during coal evolution:A density functional theory study

The formation mechanism of methane （CH4） during coal evolution has been investigated by density functional theory （DFT） of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane （CBM）. Ethylbenzene （A） and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene （B） have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal （R）, according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH4 is the dominant path for the formation of CH4 from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Formation mechanism of methane during coal evolution: A density functional theory study

The formation mechanism of methane (CH₄) during coal evolution has been investigated by density functional theory (DFT) of quantum chemistry. Thermogenic gas, which is generated during the thermal evolution of medium rank coal, is the main source of coalbed methane (CBM). Ethylbenzene (A) and 6,7-dimethyl-5,6,7,8-tetrahydro-1-hydroxynaphthalene (B) have been used as model compounds to study the pyrolysis mechanism of highly volatile bituminous coal (R), according to the similarity of bond orders and bond lengths. All possible paths are designed for each model. It can be concluded that the activation energies for H-assisted paths are lower than others in the process of methane formation; an H radical attacking on β-C to yield CH₄ is the dominant path for the formation of CH₄ from highly volatile bituminous coal. In addition, the calculated results also reveal that the positions on which H radical attacks and to which intramolecular H migrates have effects on methyl cleavage.     

Exchange and correlation energy in density functional theory

Several different versions of density functional theory (DFT) that satisfy Hohenberg–Kohn theorems are characterized by different definitions of a reference or model state determined by an N‐electron ground state. A common formalism is developed in which exact Kohn–Sham equations are derived for standard Kohn–Sham theory, for reference‐state density functional theory, and for unrestricted Hartree–Fock (UHF) theory considered as an exactly soluble model Hohenberg–Kohn theory. A natural definition of exchange and correlation energy functionals is shown to be valid for all such theories. An easily computed necessary condition for the locality of exchange and correlation potentials is derived. While it is shown that in the UHF model of DFT the optimized effective potential (OEP) exchange satisfies this condition by construction, the derivation shows that this condition is not, in general, sufficient to define an exact local exchange potential. It serves as a test to eliminate proposed local potentials that are not exact for ground states. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 521–525, 2000     

Au_n团簇催化水煤气变换反应机理的密度泛函理论研究

利用密度泛函理论(DFT)研究了Au10、Au13和Au20三类团簇的稳定性和对水煤气变换(WGSR)反应的催化活性,考察了各物质在Aun团簇上的吸附行为和微观反应机理。结果表明,三类Aun团簇的稳定性顺序为Au10Au13Au20,而Aun团簇中电子离域性及吸附能力大小趋势为Au13Au10Au20。在三类Aun团簇上,水煤气变换反应的控速步骤均为H2O的解离,但其反应机理路径有所不同。Au10团簇上为羧基机理,COOH*中间体直接解离;Au13团簇上为氧化还原机理,两个OH*发生歧化反应;Au20团簇上为羧基机理,COOH*和OH*发生歧化反应。通过对三类团簇上的最佳反应路径进行比较发现,Au13团簇在低温下具有较好的催化活性。     

污泥热解中HCN与CaO的反应机理:密度泛函理论研究

采用密度泛函理论对污泥热解中CaO与HCN在低温段的反应进行了研究。在B3LYP/6-311++(3df,2p)水平上计算得到了反应路径上各驻点的几何构型与频率,并在此构型上使用CCSD(T)/cc-pVQZ进行单点能计算。结果表明,两个HCN分子吸附于CaO后,质子发生转移时出现反应路径中最大能垒(310.33 kJ/mol)。使用经典过渡态理论拟合了反应中各步骤的阿累尼乌斯公式,计算了三种典型温度下各步骤的反应速率,发现质子转移为该反应的决速步骤,且温度越高CaO对HCN的作用效果越好。     

Gas-phase acidity of D-glucose. A density functional theory study

The gas-phase acidity of D-glucopyranose was studied by means of B3LYP calculations combined with 6-31G(d,p) or 6-31+G(d,p) standard basis sets. For each anomer, deprotonation of the various primary and secondary hydroxyl groups was considered. As in solution, the anomeric hydroxyl is found to be the most acidic for both anomers, but only when the 6-31+G(d,p) basis set is used for geometry optimization. Deprotonation of the anomeric hydroxyl induces an important C(1)--O endocyclic bond elongation and subsequently promotes an energetically favored ring-opening process as attested by the very small calculated activation barriers. The results also suggest that interconversion between the various deprotonated alpha- and beta-anomers may easily occur under slightly energetic conditions. B3LYP/6-311+G(2df,2p) calculations led to the an absolute gas-phase acidity of deltaacidGo(298)(alpha-D-glucose) = 1398 kJ mol(-1). This estimate matches well the only experimental value available to date. Finally, this study again confirms that the use of diffuse functions on heavy atoms is necessary to describe anionic systems properly and to achieve good relative and absolute gas-phase acidities.