Density functional calculations on cyclodextrins

Conformations of α-, β-, and γ-CDs under anhydrous conditions in the gas phase were investigated by a density functional method, B3LYP/6-31G(d,p). These calculations resulted in several symmetric conformations with different energies. The lowest energy conformations contain two rings of homodromic hydrogen bonds and are referred to “one-gate-closed” conformations. Different orientations of hydrogen bonds lead to four minima. Other conformational minima were found for “open” conformations which correspond to some extent to experimentally determined structures.     

黄嘌呤及其互变异构体的密度泛函理论研究

嘌呤碱及其衍生物在生物系统中起重要作用。对人具有兴奋和利尿作用的茶碱和咖啡碱就是黄嘌呤的甲基衍生物。黄嘌呤存在多种互变异构体,从理论计算的角度研究这些互变异构体的几何结构、电子结构及相对稳定性,进一步研究溶剂对其结构和性质的影响是有意义旧。密度泛函理论方法既考虑了电子相关,又较其它CI（组态相互作用）或MPn（n级微扰）方法节省机时。其计算结果较好,被广泛应用于研究各种化合物。本文采用密度泛函B3LYP／6—311G方法对14种黄嘌呤可能的互变异构体（见图1）,分别在气相和水相中进行几何构型全自由度优化和能量计算,讨论了异构体的相对稳定性,水的溶剂化作用对异构体的能量、几何构型、电荷分布和偶极矩的影响,探讨了溶剂极性对异构体的能量和偶极矩的影响。     

Density functional theory study of the Jahn-Teller effect and spin-orbit coupling for copper and gold trimers

The Born-Oppenheimer potential energy hypersurfaces of copper and gold trimers were calculated using density functional theory with an analytic potential. The calculated Jahn-Teller distortion energies, pseudorotation barriers, dissociation, and isomerization energies for the two trimers are discussed. Global minima from the surfaces were optimized using the density functional theory method as well as the coupled cluster-singles-doubles-with-triples energies technique. The agreement of the optimized structures with the analytic potential was very good. The Mulliken population analysis compared favorably with the experimental electron spin resonance results. Spin-orbit coupling was subsequently included and the effect was significant for gold, but negligible for copper. The spin-orbit effect suppressed the Jahn-Teller distortion of the gold trimer, and the potential surface with the spin-orbit effect included was also obtained. The spin-orbit splitting for the D(3h) geometry of the gold trimer was in excellent agreement with the most recent infrared spectroscopic results.     

Density functional calculations of surface free energies

We propose a general method of thermodynamic integration to find the free energy of a surface, where our integration parameter is taken to be the strain on the unit cell of the system (which in the example presented in this paper is simply the extension of the unit cell along the normal to the surface), and the integration is performed over the thermal average stress from a molecular dynamics run. In order to open up a vacuum gap in a continuous and reversible manner, an additional control interaction has been introduced. We also use temperature integration to find a linear relation for the temperature dependence of the free surface energy. These methods have been applied to the titanium dioxide (110) surface, using first principles density functional theory. A proof of principle calculation for zero temperature shows excellent agreement between the integral calculation and the difference in energy calculated by the DFT program. Calculations that have been performed at 295 and 1000 K give excellent agreement between the two integration methods.     

Density functional calculations for4He droplets

A novel density functional, which accounts correctly for the equation of state, the static response function and the phonon-roton dispersion in bulk liquid helium, is used to predict static and dynamic properties of helium droplets. The static density profile is found to exhibit significant oscillations, which are accompanied by deviations of the evaporation energy from a liquid drop behaviour in the case of small droplets. The connection between such oscillations and the structure of the static response function in the liquid is explicitly discussed. The energy and the wave function of excited states are then calculated in the framework of time dependent density functional theory. The new functional, which contains backflow-like effects, is expected to yield quantitatively correct predictions for the excitation spectrum also in the roton wave-length range.     

PFI-ZEKE photoelectron spectra of the methane cation and the dynamic Jahn-Teller effect

High resolution pulsed-field-ionization (PFI) zero-kinetic-energy (ZEKE) photoelectron spectroscopy has been used to record the photoelectron spectra of CH4, CDH3, CD2H2 and CD4. The observed extensive progression of rotationally resolved transitions between 100,800 cm-1 and 104,100 cm-1 reveals for the first time the complex energy level structure of the methane cation. The high resolution enabled the determination of accurate values for the adiabatic ionization potentials of the different isotopomers. Based on a simple one-dimensional model for the pseudorotation in the different isotopomers, progress has been made towards the understanding of the Jahn-Teller effect at low energies. The static Jahn-Teller distortion in the ion could be determined directly from the vibrationless photoelectron transition in CD2H2. The analysis of the rotational structure in this spectrum with a rigid rotor model leads to an approximate experimental C2v structure. The dynamics of the other methane isotopomers near the adiabatic ionization potentials is dominated by large amplitude vibrational motions between equivalent structures. The corresponding ground state tunneling motions takes place on a picosecond time scale.     

Density functional response theory calculations of three-photon absorption

Three-photon absorption probabilities delta(3PA) have been calculated through application of a recently derived method for cubic response functions within density functional theory (DFT). Calculations are compared with Hartree-Fock (HF) and with a coupled cluster hierarchy of models in a benchmarking procedure. Except for cases having intermediate states near resonance, density functional theory is demonstrated to be in sufficient agreement with the highly correlated methods in order to qualify for predictions of delta(3PA). For the larger systems addressed, a set of acceptor A and donor D substituted pi-conjugated systems formed by trans-stilbene and dithienothiophene (DTT), we find noticeable differences in the magnitude of delta(3PA) between HF and DFT, although similar trends are followed. It is shown that the dipolar structures, TS-AD and DTT-AD, have substantially larger delta(3PA) than other types of modifications which is in accordance with observations for two-photon absorption. This is the first application of density functional theory to three-photon absorption beyond the use of few-state models.     

Density functional calculations of the pseudorotational flexibility of tetrahydrofuran

The flexibility of the five-membered ring in tetrahydrofuran was investigated using quantum mechanical methods involving density functional, Hartree-Fock, and many-body perturbation theory (MP2, MP4) calculations. We found that motion along the pseudorotational path of tetrahydrofuran is nearly free. The 0.1 kcal/mol energy barrier for pseudorotation, calculated at the highest MP4(SDQ)/6-311++G(2d,p)//MP2/6-311++G(2d,p) level of theory, agrees well with the experimental value of 0.16±0.03 kcal/mol. Similar results were obtained with the S-VWN, B3-LYP and B-LYP density functional calculations using the 6-31G(d) set of atomic orbitals. Also the density functional dipole moments and geometries were in good agreement with both the MP2 and experimental benchmarks. However, all density functional methods that utilized the default integration grid in the Gaussian 94 program were found to provide false stationary points of the C ₁ symmetry near the pseudorotational angle of 100°. These stationary points disappeared when a denser spherical-product grid was used. Overall, the hybrid B3-LYP functional was found to be the most promising quantum mechanical method for the modeling of biomolecules containing the furanose ring. Received: 17 June 1997 / Accepted: 20 November 1997     

Density functional calculations on triply excited states of lithium isoelectronic sequence

Triply excited states of many-electron atomic systems are characterized by the presence of strong electron correlation, closeness to more than one threshold, and degeneracy with many continua; therefore, they offer unusual challenges to theoretical methodologies. In the present article, we computed with reasonable accuracy all the n=2 intrashell triply excited states (2s²2p ²P; 2s2p^{2 2}D, ⁴P, ²P, ²S; and 2p^{3 2}D, ²P, ⁴S) of three-electron atomic systems (Z=2, 3, 4, 6, 8, 10) by using a density functional formalism developed recently in our laboratory, based on the nonvariational Harbola–Sahni exchange potential in conjunction with a parametrized local Wigner and Lee–Yang–Parr correlation potentials. Nonrelativistic energies and densities are obtained by solving a Kohn–Sham-type differential equation. The calculated results are compared with available experimental and other theoretical data. The 2p³(⁴S)→1s2p²(⁴P) transition wavelength for the isoelectronic series is also computed. The overall good agreement of our results with the literature data indicates the reliability of the present density functional methodology for excited states of many-electron systems. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65 : 317–332, 1997     

Density functional calculations of difluorodiazete structures with Gaussian-orbital-type approach

The comparison of local nonlocal and hybrid DFT methods with RHF , MP 2, CCSD , and CPF ab initio methods in generating geometries and relative energies of cis- and trans-difluorodiazete, SVWN , BLYP , BP 86, BECKE 3LYP , and BECKE 3P 86 DFT methods with 6-311 + g(2d) and 6-311 + + g(3df) basis sets. The geometries generated with RHF ab initio models are quite different from experimental values and energy evaluation prefers the wrong isomer. The hybrid methods give superior geometries while energies evaluated with nonlocal DFT methods are better than the one obtained with MP 2 or CCDS ab initio methods. The results suggest DFT as the method of choice of studying similar systems. © 1996 John Wiley & Sons, Inc.     

The Jahn-Teller effect in the triply degenerate electronic state of methane radical cation

A quantum dynamics study is performed to examine the complex nuclear motion underlying the first photoelectron band of methane. The broad and highly overlapping structures of the latter are found to originate from transitions to the ground electronic state, X(2)T(2), of the methane radical cation. Ab initio calculations have also been carried out to establish the potential energy surfaces for the triply degenerate electronic manifold of CH(4)(+). A suitable diabatic vibronic Hamiltonian has been devised and the nonadiabatic effects due to Jahn-Teller conical intersections on the vibronic dynamics investigated in detail. The theoretical results show fair accord with experiment.     

Density functional theory calculations of the effect of fluorine substitution on the cyclobutylcarbinyl to 4-pentenyl radical rearrangement

The effects of fluorine substitution on the cyclobutylcarbinyl to 4-pentenyl radical rearrangement and on the strain of cyclobutane have being studied using density functional theory, the ring-opening being modestly inhibited and the strain generally not greatly affected. Perfluorocyclobutane is predicted to have 6 kcal/mol less strain than cyclobutane. Cyclizations of 1,1,2,2-tetrafluoro- and 1,1,2,2,3,3-hexafluoro-4-pentenyl radicals should be significantly enhanced ( approximately 2400 times faster) relative to the parent system. The calculations are consistent with the few experimental data available.     

Density functional calculations of the physicochemical properties of formamidyl radicals

The geometric, spectroscopic, and thermodynamic parameters of the HNC(O)H radical were studied by the DFT B3L YP/6-311++G(3df, 3pd) method. The structure of its conformers was established. Electron and spin density distributions were analyzed. The potential function of internal hindered rotation was calculated. The enthalpies of dissociation were determined for the O-H bond in HNC(OH)H and N-H bond in H₂NC(O)H.     

Pd金属表面CO吸附态的密度泛函计算及应用

通过对CO在Pd表面上形成的各种化学吸附态的理论计算,借助B3LYP／3—21G＊方法,确定了各种吸附态Pdn-CO（n=1-5,7,9）的优化几何构型、相对稳定性、反应活性和吸附性质。其中μ3-Pd,CO和μ4-Pd4CO比线式和桥式更易使CO活化,而且相对难解吸,表现出较好的催化性能。论文还就实验FT-IR谱峰,模拟了一些未见实验报道的吸附态,同时讨论了其稳定性和理论伸展振动频率。最后运用多组态相互作用（CASS-CF／3-21G＊）计算了主要吸附态的离解能,得到Pdn-CO较Pdn-OC稳定的结论。根据各吸附态的稳定性和对CO的活化程度,确定了桥式态IR吸收是实验跟踪反应的最佳吸收带。     

Effects of solvent on weak halogen bonds: Density functional theory calculations

In recent years, many applications of solution‐phase halogen bonding in anion recognition, catalysis, and pseudorotaxane formation have been reported. Moreover, a number of thermodynamic data of halogen bonding interactions in organic solution are now available. To obtain detailed information of the influence of the surrounding medium on weak halogen bonds, a series of dimeric complexes of halobenzene (PhX) with three electron donors (H₂O, HCHO, and NH₃) were investigated by means of DFT/PBE calculations in this work. The PCM implicit solvation approach was utilized to include the effects of three solvents (cyclohexane, chloroform, and water) as representatives for a wide range of dielectric constant. In some cases, halogen‐bond distances are shown to shorten in solution, accompanied by concomitant elongation of the C? X bonds. For the remaining systems, the intermolecular distances tend to increase or remain almost unchanged under solvent effects. In general, the solvent has a slight destabilizing effect on weak halogen bonds; the strength order of halogen bonds observed in vacuum remains unchanged in liquid phases. Particularly, the interaction strength attenuates in the order I > Br > Cl in solution, consistent with the experimental measurements of weak halogen bond door abilities. The similarities between halogen and hydrogen bonding in solution were also elucidated. The results presented herein would be very useful in future applications of halogen bonding in molecular recognition and medicinal chemistry. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Density functional calculations of NMR chemical shifts and ESR g-tensors

An overview is given on recent advances of density functional theory (DFT) as applied to the calculation of nuclear magnetic resonance (NMR) chemical shifts and electron spin resonance (ESR) g-tensors. This is a new research area that has seen tremendous progress and success recently; we try to present some of these developments. DFT accounts for correlation effects efficiently. Therefore, it is the only first-principle method that can handle NMR calculations on large systems like transition-metal complexes. Relativistic effects become important for heavier element compounds; here we show how they can be accounted for. The ESR g-tensor is related conceptually to the NMR shielding, and results of g-tensor calculations are presented. DFT has been very successful in its application to magnetic properties, for metal complexes in particular. However, there are still certain shortcomings and limitations, e.g., in the exchange-correlation functional, that are discussed as well. Received: 24 October 1997 / Accepted: 19 December 1997     

Density functional theory calculations of pressure effects on the vibrational structure of alpha-RDX

Pressure effects on the vibrational structure of alpha-RDX were examined using density functional theory (DFT) up to 4 GPa. The calculated vibrational frequencies at ambient conditions are in better agreement with experimental data than are previous single molecule calculations. The calculations showed the following pressure-induced changes: (i) larger shifts for lattice modes and for internal modes associated with the CH(2) and NO(2) groups as compared to the pressure shifts for modes associated with the triazine ring, (ii) enhancement of mixing between different vibrations, for example, between NN stretching and CH(2) scissor, wagging, twisting vibrations, and (iii) increase in mixing between translational lattice vibrations and the NO(2) wagging vibrations, reducing the distinction between internal and lattice modes. The calculated volume and lattice constants at ambient pressure are larger than the experimental values, due to the inability of the present density functional approach to correctly account for van der Waals forces. Consequently, the pressure-induced frequency shifts of many modes deviate substantially from experimental data for pressures below 1 GPa. With increasing pressure, both the lattice constants and the frequency shifts agree more closely with experimental values.     

Density functional calculations on dissociation reactions of radical anions of 5-fluorouracil derivatives

Fragmentation reactions upon electron attachment to 5-fluorouracil with CH2R substituents at N1 have been evaluated by means of density functional calculations. The present results show that electron attachment to R = F, HC=O or CN derivatives follows a stepwise pathway with radical anions as intermediates. For these compounds, the most stable species formed is the pi radical anion which bears an unpaired spin density at the C6=C5-C4=O pi-conjugated system of the uracil ring. Cleavage of the N1-CH2R or N1CH2-R bond of these intermediates proceeds through the mixing of the pi and sigma states by means of proper geometrical fluctuations along the reaction coordinate. No sigma radical anion could be characterised on any of these sigma basal potential surfaces. A noticeable decrease in the activation energy for the N1-CH2R bond dissociation was observed for R = H-C=O or CN. Therefore, such derivatives with unsaturated groups positioned vicinal to the N1-C1' bond are identified as targets for the development of novel radiation-activated antitumour drugs. On the other hand, the electron transfer to the compounds with R = Cl, Br is dissociative, i.e. it occurs without the mediation of radical anions. For compounds with R = halides or R = NO2, the fragmentation of the N1CH2-R bond is the preferred dissociation pathway.     

Density functional theory calculations for two-dimensional silicene with halogen functionalization

The electronic structures and band gaps of silicene (the Si analogue of graphene) adsorbed with halogen elements are studied using the density functional theory based screened exchange local density approximation method. It is found that the band gaps of silicene adsorbed with F, Cl, Br and I have a nonmonotonic change as the periodic number of the halogen elements increases. This is attributed to the transfer of contributions to band gaps from Si-Si bonding to Si-halogen bonding.