Local-scaling transformation version of density functional theory

The local-scaling transformation version of density functional theory (LS-DFT ) is reviewed. It is shown that in the context of LS-DFT it is possible to construct N-representable energy density functionals and that the theory provides systematic ways for calculating strict upper bounds to the exact energies. The importance of the concept of “orbit” in LS-DFT is indicated and several approaches leading to intraorbit and interorbit optimization are discussed. Results of the application of these optimization procedures to the determination of upper bounds for the ground-state energy of the beryllium atom are given. Also, numerical results are reported on the use of local scaling transformations for the direct solution of the Kohn-Sham equations via the density-constrained minimization of the kinetic energy of a noninteracting system. © 1995 John Wiley & Sons, Inc.     

An improved theoretical approach to the empirical corrections of density functional theory

An empirical correction to density functional theory (DFT) has been developed in this study. The approach, called correlation corrected atomization–dispersion (CCAZD), involves short- and long-range terms. Short-range correction consists of bond (1,2-) and angle (1,3-) interactions, which remedies the deficiency of DFT in describing the proto-branching stabilization effects. Long-range correction includes a Buckingham potential function aiming to account for the dispersion interactions. The empirical corrections of DFT were parameterized to reproduce reported ΔH _f values of the training set containing alkane, alcohol and ether molecules. The ΔH _f of the training set molecules predicted by the CCAZD method combined with two different DFT methods, B3LYP and MPWB1K, with a 6-31G* basis set agreed well with the experimental data. For 106 alkane, alcohol and ether compounds, the average absolute deviations (AADs) in ΔH _f were 0.45 and 0.51 kcal/mol for B3LYP- and MPWB1K-CCAZD, respectively. Calculations of isomerization energies, rotational barriers and conformational energies further validated the CCAZD approach. The isomerization energies improved significantly with the CCAZD treatment. The AADs for 22 energies of isomerization reactions were decreased from 3.55 and 2.44 to 0.55 and 0.82 kcal/mol for B3LYP and MPWB1K, respectively. This study also provided predictions of MM4, G3, CBS-QB3 and B2PLYP-D for comparison. The final test of the CCAZD approach on the calculation of the cellobiose analog potential surface also showed promising results. This study demonstrated that DFT calculations with CCAZD empirical corrections achieved very good agreement with reported values for various chemical reactions with a small basis set as 6-31G*.     

An average-of-configuration method for using Kohn-Sham density functional theory in modeling ligand-field theory

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d(q)() model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d(2) model for the tetrahedral complexes VCl(4)(-) and VBr(4)(-) and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d(2)() model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl(4)(-) and VBr(4)(-) are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F(-)() among the halides corroborated for both series.     

A density functional theory investigation on the formation mechanisms of DNA interstrand crosslinks induced by chloroethylnitrosoureas

Chloroethylnitrosoureas (CENUs) are an important family of alkylating agents used in the clinical treatment of cancer. Their anticancer mechanism primarily involves the formation of DNA interstrand crosslinks (ICLs) induced by the chloroethyldiazonium ion derived from the decomposition of CENUs. In this work, the mechanism for the formation of ICLs was investigated by density functional theory (DFT) with B3LYP, wB97XD, and M062X functinoals using conductor‐like polarizable continuum model solvent model. Three pathways leading to the formation of three types of G–C crosslinks were compared. G(N1)–C(N3) crosslink is predicted to be the dominant crosslinking product other than G(O⁶)–C(N⁴) and G(N²)–C(O²) crosslinks, which is consistent with the previous results obtained from QM/MM computations. The results indicate that the formation of the G(N1)–C(N3) crosslink via pathway A is the most favorable mechanism from both kinetic and thermodynamic standpoints. In this pathway, the chloroethyldiazonium ion alkylates guanine on the O⁶ site followed by intramolecular cyclization to form O⁶,N1‐ethanoguanine ( 4 ). The cytosine then reacts with intermediate 4 on the C^α atom to yield the G(N1)–C(N3) crosslink. This work provides reasonable explanations for the supposed mechanism of CENUs‐induced ICLs formation obtained from experimental investigations. © 2012 Wiley Periodicals, Inc.     

Role of four-membered rings in C32 fullerene stability and mechanisms of generalized Stone-Wales transformation: a density functional theory investigation

Density functional theory (DFT) methods have been applied to study C(32) fullerenes built from four-, five-, and six-membered rings. The relative energies of pure C(32) fullerenes have been evaluated to locate three most stable structures, 32:D(4d) with two squares, 1:D(3) without square and 5:C(s) with one square. Structural analysis reveals that there is a rearrangement pathway between the lowest energy classical isomer 1:D(3) and the lowest energy non-classical isomer 32:D(4d), and 5:C(s) behaves just as an intermediate between them. The kinetic processes of generalized Stone-Wales transformation (GSWT) with four-membered rings have been explored and two distinct reaction mechanisms are determined by all the transition states and intrinsic reaction coordinates with PBE1PBE/6-31G(d) approach for the first time. One mechanism is the concerted reaction with a rotating dimer closed to the cage surface and another is the stepwise reaction with a carbene-like sp(3) structure, whereas the latter is sorted into two paths based on four-membered ring vanishing before or after the formation of the carbene-like structure. It is indicated that there is no absolute preference for any mechanism, which depends on the adaptability of different reactants on the diverse mechanisms. Furthermore, it's found that the interconversion process with the participation of squares is more reactive than the rearrangement between C(60)_I(h) and C(60)_C(2v), implying some potential importance of non-classical small fullerenes in the fullerene isomerization.     

3-乙酰基-8-叔丁基香豆素晶体结构及密度泛函理论研究

本文合成了3-乙酰基-8-叔丁基香豆素,并通过X-射线单晶衍射法测定分子结构,随后进行红外、核磁共振、紫外可见吸收光谱表征,并通过密度泛函理论(DFT)研究晶体中的分子间作用,模拟光谱并预测表面活性位点。结果表明,分子为大共轭平面结构,在晶体中主要以π-π堆积作用和氢键作用结合,结合能分别为17. 2和3. 9 kcal/mol。分子在近紫外可见光范围内的最大吸收波长在310nm,摩尔消光系数为16000L·mol-1·cm-1,主要对应苯环上π电子向内酯环以及羰基氧上的跃迁。该分子6号位碳最易发生芳环上亲电取代反应,内酯可发生水解、氨解等反应,苯环上氢、羰基氧均可形成氢键等弱相互作用。     

氢化可的松和表氢化可的松的密度泛函理论研究

采用密度泛函理论B3LYP/6-31G和B3LYP/6-311G*方法优化了氢化可的松和表氢化可的松的几何结构,利用优化的结构得到了氢化可的松和表氢化可的松的原子净电荷、总能量及前沿分子轨道组成.基于简谐振动分析求得了氢化可的松和表氢化可的松的红外光谱频率和强度,由统计热力学分析得到了热力学函数;进而确定了氢化可的松和...     

An ab initio and density functional theory study of radical-clock reactions

Density functional theory (DFT) and ab initio (CBS-RAD) calculations have been used to investigate a series of "radical clock" reactions. The calculated activation energies suggest that the barriers for these radical rearrangements are determined almost exclusively by the enthalpy effect with no evidence of significant polar effects. The ring-closure reactions to cyclopentylmethyl radical derivatives and the ring opening of cyclopropylmethyl radicals give different correlations between the calculated heat of reaction and barrier, but the two types of reaction are internally consistent.     

Density-gradient analysis for density functional theory: Application to atoms

We present an analysis of local or semilocal density functionals for the exchange-correlation energy by decomposing them into their gradients r_s (local Seitz radius), ζ (relative spin polarization), and s (reduced density gradient). We explain the numerical method pertaining to this kind of analysis and present results for a few atoms and ions. The atomic shell structure is prominent, and only the ranges 0 < r_s < 10 and 0 < s < 3 are important. The low-density and large-gradient domains, where the approximations for the exchange-correlation energy are least trustworthy, have very little weight. © 1997 John Wiley & Sons, Inc.     

Generalized density functional theory for degenerate states

An extension of density functional theory is proposed for degenerate states. There are suitably selected basic variables beyond the subspace density. Generalized Kohn-Sham equations are derived. A direct method is proposed to ensure the fixed value of ensemble quantities. Then the Kohn-Sham equations are similar to the conventional Kohn-Sham equations. But the Kohn-Sham potential is different for different ensembles. A simple local expression is proposed for the correlation energy.     

Incremental solver for orbital-free density functional theory

First-principle calculations are still a challenge since they require a great amount of computational time. In this article, we introduce a new algorithm to perform orbital-free density functional theory (OF-DFT) calculations. Our new algorithm focuses computational efforts on important parts of the particle system, which, in the context of adaptively restrained particle simulations (ARPS) allows us to accelerate particle simulations. © 2019 Wiley Periodicals, Inc.     

Structure of the ammonia dimer studied by density functional theory

Self-consistent Kohn–Sham density functional calculations have been carried out to study the structure of the ammonia dimer. The local-density approximation yields unusually large binding energy and short internitrogen distance compared with the experimental and more accurate theoretical data. The results from the Becke–Perdew gradient-corrected functionals are generally in good agreement with those at the SCF MP 2 level when the geometry is fully optimized with various large basis sets. With our best estimation, the staggered quasi-linear structure (C_s) is 0.6 kcal/mol lower in energy than the symmetric cyclic one (C_2h). The hydrogen-bonded N—H bond in the staggered quasi-linear structure is found to be 0.008 Å longer than the N—H bond in ammonia. In our calculations, we could not find the minima on the energy surface corresponding to the two asymmetric cyclic structures suggested by microwave spectra and coupled pair functional calculations. © 1994 John Wiley & Sons, Inc.     

Applying the concepts of density functional theory to simple systems

Equations are derived for the chemical potential and local hardness of the ground states of helium and the related two electron ions. With these properties it is possible to correct the energies of the simple single‐zeta wave functions to the nearly exact values. The calculations are simple for these simple systems. In principle, it is possible to extend this method to all atoms and molecules. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Photosensitization mechanisms of triplet excited state beta-lapachone. A density functional theory study

Beta-Lapachone is a natural product with multiple pharmacological activities and mechanistic studies indicated that reactive oxygen species (ROS) generated by beta-lapachone play significant roles in its pharmacological actions. As photosensitization is an important ROS-generating pathway, in the present work, the photosensitization mechanisms of beta-lapachone are explored on the basis of density functional theory estimated triplet excited state characters. Starting from triplet excited state beta-lapachone, the possible generating pathways of 1O2 and O2*- are elucidated and the solvent effects on the photosensitizing reactions are also discussed.     

Supramolecular binding thermodynamics by dispersion-corrected density functional theory

The equilibrium association free enthalpies ΔG(a) for typical supramolecular complexes in solution are calculated by ab initio quantum chemical methods. Ten neutral and three positively charged complexes with experimental ΔG(a) values in the range 0 to -21?kcal?mol(-1) (on average -6?kcal?mol(-1) ) are investigated. The theoretical approach employs a (nondynamic) single-structure model, but computes the various energy terms accurately without any special empirical adjustments. Dispersion corrected density functional theory (DFT-D3) with extended basis sets (triple-ζ and quadruple-ζ quality) is used to determine structures and gas-phase interaction energies (ΔE), the COSMO-RS continuum solvation model (based on DFT data) provides solvation free enthalpies and the remaining ro-vibrational enthalpic/entropic contributions are obtained from harmonic frequency calculations. Low-lying vibrational modes are treated by a free-rotor approximation. The accurate account of London dispersion interactions is mandatory with contributions in the range -5 to -60?kcal?mol(-1) (up to 200?% of ΔE). Inclusion of three-body dispersion effects improves the results considerably. A semilocal (TPSS) and a hybrid density functional (PW6B95) have been tested. Although the ΔG(a) values result as a sum of individually large terms with opposite sign (ΔE vs. solvation and entropy change), the approach provides unprecedented accuracy for ΔG(a) values with errors of only 2?kcal?mol(-1) on average. Relative affinities for different guests inside the same host are always obtained correctly. The procedure is suggested as a predictive tool in supramolecular chemistry and can be applied routinely to semirigid systems with 300-400 atoms. The various contributions to binding and enthalpy-entropy compensations are discussed.     

Real-time propagation time-dependent density functional theory study on the ring-opening transformation of the photoexcited crystalline benzene

Mechanism of the ring-opening transformation in the photoexcited crystalline benzene is investigated on the femtosecond scale by a computational method based on the real-time propagation (RTP) time-dependent density functional theory (TDDFT). The excited-state dynamics of the benzene molecule is also examined not only for the distinction between the intrinsic properties of molecule and the intermolecular interaction but for the first validation using the vibration frequencies for the RTP-TDDFT approach. It is found that the vibration frequencies of the excited and ground states in the molecule are well reproduced. This demonstrates that the present method of time evolution using the Suzuki-Trotter-type split operator technique starting with the Franck-Condon state approximated by the occupation change of the Kohn-Sham orbitals is adequately accurate. For the crystalline benzene, we carried out the RTP-TDDFT simulations for two typical pressures. At both pressures, large swing of the C-H bonds and subsequent twist of the carbon ring occurs, leading to tetrahedral (sp3-like) C-H bonding. The nu4 and nu16 out-of-plane vibration modes of the benzene molecule are found mostly responsible for these motions, which is different from the mechanism proposed for the thermal ring-opening transformation occurring at higher pressure. Comparing the results between different pressures, we conclude that a certain increase of the intermolecular interaction is necessary to make seeds of the ring opening (e.g., radical site formation and breaking of the molecular character) even with the photoexcitation, while the hydrogen migration to fix them requires more free volume, which is consistent with the experimental observation that the transformation substantially proceeds on the decompression.     

Orbital-free density functional theory applied to NaAlH4

We present the application of orbital-free density functional theory (OF-DFT) to NaAlH(4), a potential hydrogen storage material, and related systems. Although the simple Al and NaH structures are reproduced reasonably well by OF-DFT, the approach fails for the more complex NaAlH(4) structure. Calculations on AlH(3) show that the failure to describe the Al-H interaction is related to the kinetic energy functionals used rather than the local pseudopotentials which are required within the OF-DFT approach. Thus, systems such as NaAlH(4) present a challenge which awaits the development of more reliable orbital-free kinetic energy functionals.     

An atomic scale mechanism for the antimalarial action of chloroquine from density functional theory calculations

The X-ray crystal structures of complexes between the antimalarial drugs quinine, quinidine and halofantrine and their biological target, iron(III) ferriprotoporphyrin IX (FePPIX), have been reported in the literature (de Villiers et al. in ACS Chem Biol 7:666, 2012; J Inorg Biochem 102:1660, 2008) and show that all three drugs utilize their zwitterionic alkoxide forms to coordinate to the iron atom via Fe–O bonds. In this work, density functional theory calculations with implicit solvent corrections have been used to model the energetics of formation of these complexes. It is found that the cost of formation of the active zwitterionic form of each drug is more than offset by the energy of its binding to FePPIX, such that the overall energies for complexation of all three drugs with FePPIX are moderately favourable in water, and rather more favourable in n-octanol as solvent. The calculations have been extended to develop an analogous model for the complex between FePPIX and chloroquine, whose structure is not presently known from experiment.     

Model for acetylene reduction by nitrogenase derived from density functional theory

The catalytic cycle of acetylene reduction at the FeMo cofactor of nitrogenase has been investigated on the basis of density functional theory. C2H2 binds to the same site as N2, but it binds to a less reduced state of the cofactor. In a manner similar to that of N2 binding, one of the sulfur bridges opens during acetylene binding. The model explains the strong noncompetitive inhibition of N2 reduction by C2H2 and the weak competitive inhibition of C2H2 reduction by N2. Our proposed mechanism is consistent with experimentally observed stereoselectivity and the ability of C2H2 to suppress H2 production by nitrogenase.