Investigation of spin-flip reactions of Zr + CH3CN by relativistic density functional theory

To explore the details of the reaction mechanisms of Zr atoms with acetonitrile molecules, the triplet and singlet spin-state potential energy surfaces have been investigated. Density functional theory (DFT) with the relativistic zero-order regular approximation at the PW91/TZ2P level has been applied. The complicated minimum energy reaction path involves four transition states (TS), stationary states 1-5 and one spin inversion (indicated by ?): (3)Zr + NCCH(3) → (3)Zr-η(1)-NCCH(3) ((3)1) → (3)TS(1/2) → (3)Zr-η(2)-(NC)CH(3) ((3)2) → (3)TS(2/3) → (3)ZrH-η(3)-(NCCH(2)) ((3)3) → (3)TS(3/4) → CNZrCH(3) ((3)4) ? (1)TS(4/5) → CN(ZrH)CH(2) ((1)5). The minimum energy crossing point was determined with the help of the DFT fractional-occupation-number approach. The spin inversion leading from the triplet to the singlet state facilitates the activation of a C-H bond, lowering the rearrangement-barrier by 78 kJ/mol. The overall reaction is calculated to be exothermic by about 296 kJ/mol. All intermediate and product species were frequency and NBO analyzed. The species can be rationalized with the help of Lewis type formulas.     

Time-dependent density functional theory gradients in the Amsterdam density functional package: geometry optimizations of spin-flip excitations

An implementation of time-dependent density functional theory (TDDFT) energy gradients into the Amsterdam density functional theory program package (ADF) is described. The special challenges presented by Slater-type orbitals in quantum chemical calculation are outlined with particular emphasis on details that are important for TDDFT gradients. Equations for the gradients of spin-flip TDDFT excitation energies are derived. Example calculations utilizing the new implementation are presented. The results of standard calculations agree well with previous results. It is shown that starting from a triplet reference, spin-flip TDDFT can successfully optimize the geometry of the four lowest singlet states of CH₂ and three other isovalent species. Spin-flip TDDFT is used to calculate the potential energy curve of the breaking of the C?CC bond of ethane. The curve obtained is superior to that from a restricted density functional theory calculation, while at the same time the problems with spin contamination exhibited by unrestricted density functional theory calculations are avoided.     

How to determine activation energy of glass transition

The article critically reviews the current methodologies for determination of apparent activation energy of structural relaxation, ?h*, in the glass transition range. Tool–Narayanaswamy–Moynihan phenomenological model was used to simulate data for all major types of relaxation behavior, which were consequently evaluated in terms of the tested methodologies (curve-fitting, evaluation of ?h* from intrinsic cycles and evaluation of ?h* from constant heating rate cycles). Advantages and disadvantages of particular methodologies are demonstrated and thoroughly discussed. In addition, effects of various data-distortive effects influencing determination of glass transition activation energy are demonstrated and described. The discussed data-distortive effects include presence thermal gradients, improperly designed temperature programs, incorrectly applied subtractions of the thermokinetic background, or inability of the DSC instrument to perform high cooling/heating rates. Detailed guide for correct determination of ?h* from DSC measurements is introduced.     

A density functional study of chemical reactions

Density functional theory (DFT ) was used to study reactions involving small molecules. Relative energies of isomers and transition structures of diazene, formaldehyde, and methylenimine were determined using various DFT functionals and results were compared with MP 2 and MP 4 calculations. DFT reaction barriers were found to be consistently lower. For some reactions, such as OH + H₂→ H₂O + H, gradient-corrected functionals predict very low or nonexistent barriers. The hybrid Hartree–Fock–DFT adiabatic connection method (ACM ) often provides much better results in such cases. The performance of several density functionals, including ACM , was tested in calculations on over 100 atomization, hydrogenation, bond dissociation, and isodesmic reactions. The ACM functional provides consistently better geometries and reaction energetics than does any other functional studied. In cases where both HF and gradient-corrected DFT methods underestimate bond distances, the ACM geometries may be inferior to those predicted by gradient-corrected DFT methods. © 1995 John Wiley & Sons, Inc.     

一种测定功能蛋白与其配体结合参数的简单方法

以羰基二咪唑法分别将牛血清白蛋白(BSA)和β2-肾上腺素受体(β2-AR)键合在大孔硅胶上,合成两种色谱固定相。采用直接进样法测定BSA与奥美拉唑、普萘洛尔和盐酸异丙嗪的结合常数及结合位点数,β2-AR与盐酸异丙肾上腺素、沙丁胺醇和去甲肾上腺素的结合常数及结合位点数。方法可用于功能蛋白与其配体分子相互作用的研究。     

一种测定功能蛋白与其配体结合参数的简单方法

以羰基二咪唑法分别将牛血清白蛋白(BSA)和β2-肾上腺素受体(β2-AR)键合在大孔硅胶上,合成两种色谱固定相。采用直接进样法测定BSA与奥美拉唑、普萘洛尔和盐酸异丙嗪的结合常数及结合位点数,β2-AR与盐酸异丙肾上腺素、沙丁胺醇和去甲肾上腺素的结合常数及结合位点数。方法可用于功能蛋白与其配体分子相互作用的研究。     

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     

Rapidly convergent procedure to solve the density profile equation in the classical density functional theory

An efficient recursive procedure to solve the density profile equation in the classical density functional theory (DFT) using an inverse Broyden method is described. The present iterative procedure is free of calculation of the Jacobian matrix, and its inversion unavoidable for the well-known Newton-Raphson (NR) method and its variants. Numerical calculation indicates that only the approximate solution and iterative matrix of the lower bulk density case are employed as the corresponding initial guesses of the higher bulk density case, the present recursive procedure can converge quickly to the physical solution with an accuracy of epsilon = 10(-14); therefore, the procedure provides an efficient numerical algorithm for the theory in which acquirement of a density profile of high accuracy is a key step. Extensive numerical calculation shows the advantage of the present inverse Broyden method over Broyles' mixing procedure and a modified Powell hybrid algorithm (a variation of the NR method).     

Development of a finite-temperature density functional approach to electrochemical reactions

We present a computational method to calculate the electronic states of a molecule in an electrochemical environment. The method is based on our recently developed finite-temperature density functional theory approach to calculate the electronic structures at a constant chemical potential. A solvent effect is treated at the level of the extended self-consistent reaction field model, which allows considering a nonequilibrium solvation effect. An exchange-correlation functional with a long-range correction is employed in this calculation, because the functional is adjusted so that the derivative discontinuity of energy with respect to a number of electrons could be satisfied. It has been found that the derivative discontinuity condition plays a crucial role in an electrochemical system. The computational results are presented for a reaction of NO(+) + e(-) <==> NO in chemical equilibrium. Owing to the improvement in the solvation effect and the exchange-correlation functional, the calculated activation free energy is in good agreement with experimental results.     

Gradient expansion of the kinetic energy density functional: Local behavior of the kinetic energy density

Calculations with Hartree—Fock electron densities for the rare gas atoms He through Xe show that the gradient expansion for the kinetic energy functional, T[] = T₀[] + T₂[] + T₄[] + … = ∫t() dτ, approximates the kinetic energy by averaging over the shell structure present in the true local kinetic energy density, t(), and that the accuracy of the gradient expansion improves with increasing atomic number. Components of t(), t₀(), t₂() and t₄(), are exhibited and discussed. The defined function t() is everywhere positive.     

Assessment of density functional theory to calculate the phase transition pressure of ice

To assess the accuracy of density functional theory (DFT) methods in describing hydrogen bonding in condensed phases, we benchmarked their performance in describing phase transitions among different phases of ice. We performed DFT calculations of ice for phases Ih, II, III, VI and VII using BLYP, PW91, PBE, PBE-D, PBEsol, B3LYP, PBE0, and PBE0-D, and compared the calculated phase transition pressures between Ih-II, Ih-III, II-VI, and VI-VII with the 0 K experimental values of Whalley [J. Chem. Phys., 1984, 81, 4087]. From the geometry optimization of many different candidates, we found that the most stable proton orientation as well as the phase transition pressure does not show much functional dependence for the generalized gradient approximation and hybrid functionals. Although all these methods overestimated the phase transition pressure, the addition of van der Waals (vdW) correction using PBE-D and PBE0-D reduced the transition pressure and improved the agreement for Ih-II. On the other hand, energy ordering between VI and VII reversed and gave an unphysical negative transition pressure. Binding energy profiles of a few conformations of water dimers were calculated to understand the improvement for certain transitions and failures for others with the vdW correction. We conclude that vdW dispersion forces must be considered to accurately describe the hydrogen bond in many different phases of ice, but the simple addition of the R(-6) term with a small basis set tends to over stabilize certain geometries giving unphysical ordering in the high density phases.     

A simple mathematical method to determine the efficiencies of log-conical detectors

A new type of photon detector, log-conical, is proposed. The average path length traveled by an incident photon of arbitrary energy as well as the geometrical solid angle are calculated in a mathematical expression to determine the efficiencies of this detector for an arbitrarily positioned isotropic radiating point source. The off-axis effect of the source position was analyzed to demonstrate the powerful capability of the proposed method. The results are compared with those obtained using a standard 3″×3″ cylindrical detector of the same volume in order to show the enhanced efficiency of the log-conical detector.     

Accurate potential energy surfaces for hydrogen abstraction reactions: A benchmark study on the XYG3 doubly hybrid density functional

The potential energy surface (PES) for the H + CH₄ system has been constructed with the recently developed XYG3 doubly hybrid functional, while those with the standard B3LYP hybrid functional, and the Møller–Plesset perturbation theory up to the second order (MP2) are also presented for comparison. Quantum dynamics studies demonstrated that satisfactory results on the reaction probabilities and the rate coefficients can be obtained on top of the XYG3‐PES, as compared to the results based on the highly accurate, yet expensive, CCSD(T)‐PES (Li et al., J. Chem. Phys. 2015, 142, 204302). Further investigation suggested that the XYG3 functional is useful in providing accurate rate coefficients for some larger systems involving H atom abstractions. © 2017 Wiley Periodicals, Inc.     

Calculation of the exchange coupling constants of copper binuclear systems based on spin-flip constricted variational density functional theory

We have recently developed a methodology for the calculation of exchange coupling constants J in weakly interacting polynuclear metal clusters. The method is based on unrestricted and restricted second order spin-flip constricted variational density functional theory (SF-CV(2)-DFT) and is here applied to eight binuclear copper systems. Comparison of the SF-CV(2)-DFT results with experiment and with results obtained from other DFT and wave function based methods has been made. Restricted SF-CV(2)-DFT with the BH&HLYP functional yields consistently J values in excellent agreement with experiment. The results acquired from this scheme are comparable in quality to those obtained by accurate multi-reference wave function methodologies such as difference dedicated configuration interaction and the complete active space with second-order perturbation theory.     

Optimizing conical intersections of solvated molecules: the combined spin-flip density functional theory/effective fragment potential method

Solvent effects on a potential energy surface crossing are investigated by optimizing a conical intersection (CI) in solution. To this end, the analytic energy gradient has been derived and implemented for the collinear spin-flip density functional theory (SFDFT) combined with the effective fragment potential (EFP) solvent model. The new method is applied to the azomethane-water cluster and the chromophore of green fluorescent protein in aqueous solution. These applications illustrate not only dramatic changes in the CI geometries but also strong stabilization of the CI in a polar solvent. Furthermore, the CI geometries obtained by the hybrid SFDFT/EFP scheme reproduce those by the full SFDFT, indicating that the SFDFT/EFP method is an efficient and promising approach for understanding nonadiabatic processes in solution.     

Direct minimization of the energy in density functional theory

The minimization of the energy functional of the first-order density matrix γ( r , r ') is achieved using unitary transformations applied to γ. Equivalently, such transformations can be carried out also on one-electron orbitals (natural orbitals) and their occupation (integer or non-integer) numbers. The conventional local density approximation based on the electron density p( r ) is then considered as a special case. The direct minimization of the energy functional of p with respect to the parameters of the unitary transformation leads to stationary conditions that are all equivalent to the Kohn–Sham equations. Preliminary numerical tests show that the proposed algorithms for the direct minimization of the energy work in a satisfactory manner. © John Wiley & Sons, Inc.     

An extended dead-end elimination algorithm to determine gap-free lists of low energy states

Proteins are flexible systems and commonly populate several functionally important states. To understand protein function, these states and their energies have to be identified. We introduce an algorithm that allows the determination of a gap-free list of the low energy states. This algorithm is based on the dead-end elimination (DEE) theorem and is termed X-DEE (extended DEE). X-DEE is applicable to discrete systems whose state energy can be formulated as pairwise interaction between sites and their intrinsic energies. In this article, the computational performance of X-DEE is analyzed and discussed. X-DEE is implemented to determine the lowest energy protonation states of proteins, a problem to which DEE has not been applied so far. We use X-DEE to calculate a list of low energy protonation states for two bacteriorhodopsin structures that represent the first proton transfer step of the bacteriorhodopsin photocycle.     

Thomas–Fermi theory from a perturbative treatment of the hydrogenic limit energy density functional: A possible link to local density functional theory

A perturbation expansion which connects the hydrogenic limit energy density functional to the Thomas–Fermi functional is discussed. This perturbation series, where the Coulomb energy density functional is treated as the perturbation to the hydrogenic limit functional, is, in fact, the q = (N/Z) expansion of Thomas–Fermi theory. A truncated form of the first-order correction to the functional provides further insight into the model which treats the ground state energy as a local functional of the electron density.