Nuclear-electronic orbital nonorthogonal configuration interaction approach

The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented. In this framework, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and a mixed nuclear-electronic time-independent Schrodinger equation is solved with molecular orbital techniques. For hydrogen transfer systems, the transferring hydrogen is represented by two basis function centers to allow delocalization of the nuclear wave function. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wave functions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wave functions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between the two delocalized vibronic states. The hydrogen tunneling splittings calculated with the NEO-NOCI approach for the [He-H-He]+ model system with a range of fixed He-He distances are in excellent agreement with NEO-full CI and Fourier grid calculations. These benchmarking calculations indicate that NEO-NOCI is a promising approach for the calculation of delocalized, bilobal hydrogen wave functions and the corresponding hydrogen tunneling splittings.     

分子间电子耦合的简便计算方法—孤立轨道法

在两态模型近似下,运用不同的计算方法评估了面心放置苯二聚体分子间电子转移耦合矩阵元.其中,基于孤立轨道依据二聚体自洽计算得到的单电子Hamiltonian(Fock矩阵)直接求解的电子转移积分的计算方法能方便地考虑孤立轨道的非正交性所带来的影响得到准确的有效电子转移积分的数值解.在该孤立轨道方法下,基函数和分子间距对电子耦合积分的影响也被系统研究.结果表明,相对基于过渡态理论寻找"两态能量差最小"计算的精确电子耦合值,基函数D95V计算结果表现出最好距离相关性.     

过渡金属异核原子簇化学键研究 1: Ⅷ-Ⅷ, ⅥB-Ⅷ族双金属原子簇电子结构研究

本文对18个Ⅷ族双金属四面体簇和16个ⅥB-Ⅷ异金属四核簇进行了量子化学研究, 用DV-Xα方法讨论了它们的化学键、电荷转移、能级态密度。计算结果表明: Ⅷ族四面体簇需36个金属电子, 其中12个形成6个金属簇骼轨道, 24个与配体成键; ⅥB-Ⅷ异金属簇核中, 因两金属能带、电负性差异, ⅥB原子易向Ⅷ原子转移电荷, 环戊二烯基配体促进这一过程; 异金属簇能级总价带比单金属簇收缩, 而d能带比单金属簇展宽。     

The absorption coefficient of a polar liquid with solvated electrons

An equation for the absorption coefficient of a polar liquid with excess (solvated) electrons is derived. It is taken into account that (1) each excess electron can for a certain time reside on only one liquid molecule (during this time, the molecule is in the anion-resonance state), and (2) a polar liquid is electrostatically nonuniform because it has different local potentials, which can be calculated for each molecule. The probabilities of quantum movements of excess electrons in a liquid from one molecule to another caused by the absorption of photons are considered.     

Photoelectron spectra studies of organic free radicals. The nitroxide radical

The photoelectron spectra of the nitroxide radicals, di-tert-butylnitroxide (DTBN) and 2,2,6,6-tetramethyl-piperidine-N-oxyl, have been studied and molecular orbital calculations made. The adiabatic first ionization potentials were found to be 6.77 and 6.73 eV for these two nitroxide radicals respectively. Four vertical ionization potentials which are common to each nitroxide radical were attributed to ionization of the odd electron in the NO anti-bonding π orbital, oxygen lone pair electrons and NO bonding π electrons. Doublet splitting of the lone pair electron peak with different peak intensities can be quantitatively understood in terms of triplet and singlet states of the photoionized nitroxide cation.     

Structural and electronic properties of compound metal clusters

The equilibrium geometries, relative stabilities, and vertical ionization potentials of compound clusters involving Li _n , Na, Mg, and Al atoms have been calculated using ab initio self-consistent field linear combination of atomic orbitals — molecular orbital (SCF-LCAO-MO) method. The exchange energies are calculated exactly using the unrestricted Hartree-Fock (UHF) method whereas the correlation correction is included within the framework of configuration interaction involving pair excitations of valence electrons. While the later correction has no significant effect on the equilibrium geometries of clusters, it is essential for the understanding of relative stabilities. Clusters with even numbers of electrons are found to be more stable than those with odd numbers of electrons regardless of their charge state and atomic composition. The equilibrium geometries of homo-nuclear clusters can be significantly altered by replacing one of its constituent atoms with a hetero-nuclear atom. The role of electronic structure on the geometries and stabilities of compound clusters is discussed.     

Non-dipole excitation of core holes by electron impact. Multiplet splitting in CO and N2

Low-energy electron impact leads to non-dipole excitation of core electrons to triplet states. The multiples splitting in CO is in agreement with theory and shows that the 2π orbital is localized predominantly on the carbon. The splitting affects both energy-loss and Auger spectra of CO and N₂.     

Calculation of molecular electronic spectra by projected-unrestricted Hartree–Fock theory

This paper is concerned with a new application of projected-unrestricted Hartree–Fock theory, namely, the calculation of electronic spectra for symmetric molecules. The excited electronic state is represented by a single determinant whose unrestricted nature allows for orbital rearrangement relative to the self-consistent ground state. The self-consistent calculation must be followed by spin projection to obtain appropriate spin eigenstates. It was necessary to develop modified procedures for portions of the spin projection calculation because our method of constructing the wave functions produces degeneracies among the natural orbitals. Illustrative calculations using the all-valence-electron INDO approximations produced results which compared favorably with configuration-interaction treatments. The method described here should be most useful, however, in conjunction with ab initio calculations using flexible basis sets.     

Electron correlation in the GK state of the hydrogen molecule

The second excited (1)Sigma(g)(+) state of the hydrogen molecule, the so-called GK state, has a potential energy curve with double minima. At the united atom limit it converges to the 1s3d configuration of He. At large internuclear distances R, it dissociates to two separated atoms, one in the ground state and another in the 2p excited state. Radial pair density calculations and natural orbital analyses reveal unusual effect of electron correlation around the K minimum of the potential energy curve. As R>2.0 a.u., a natural orbital of sigma(u) symmetry joins the two natural orbitals of sigma(g) symmetry at smaller R. The average interelectronic distance decreases as the internuclear distance increases from R=2.0 to 3.0 a.u. Around R=3.0 a.u. the singly peaked pair density curve splits into two peaks. The inner peak can be attributed to the formation of the ionic electron configuration (1s)(2), where both 1s electrons are on the same nucleus. As the two 1s electrons run into different nuclei, one of the two 1s electrons is promoted to the 2p state, which results in the outer peak in the pair density curve. The Rydberg 1s2p configuration persists as the nuclei stretch, and becomes dominant at large R where four natural orbitals, two of sigma(g) and two of sigma(u) symmetry, become responsible.     

Model potential approaches for describing the interaction of excess electrons with water clusters: incorporation of long-range correlation effects

In this work we focus on the binding of excess electrons to water clusters, a problem for which dispersion interactions, which originate from long-range correlation effects, are especially important. Two different model potential approaches, one using quantum Drude oscillators and the other using polarization potentials, are investigated for describing the long-range correlation effects between the weakly bound excess electron and the more tightly bound electrons of the monomers. We show that these two approaches are related in that the polarization potential models can be derived from the quantum Drude model approach by use of an adiabatic separation between the excess electron and the Drude oscillators. The model potential approaches are applied to clusters containing up to 45 water monomers. Where possible, comparison is made with the results of ab initio electronic structure calculations. Overall, the polarization potential approach is found to give electron binding energies in good agreement with those from the Drude model and ab initio calculations, with the greatest discrepancies being found for "cavity-bound" anion states.     

Structure and singly occupied molecular orbital analysis of anionic tautomers of guanine

Recently, we reported the discovery of adiabatically bound anions of guanine that might be involved in the processes of DNA damage by low-energy electrons and in charge transfer through DNA. These anions correspond to some tautomers that have been ignored thus far. They were identified using a hybrid quantum mechanical-combinatorial approach in which an energy-based screening was performed on the library of 499 tautomers with their relative energies calculated with quantum chemistry methods. In the current study, we analyze the adiabatically bound anions of guanine in two aspects: (1) the geometries and excess electron distributions are analyzed and compared with anions of the most stable neutrals to identify the sources of stability; (2) the chemical space of guanine tautomers is explored to verify if these new tautomers are contained in a particular subspace of the tautomeric space. The first task involves the development of novel approaches-the quantum chemical data like electron density, orbital, and information on its bonding/antibonding character are coded into holograms and analyzed using chemoinformatics techniques. The second task is completed using substructure analysis and clustering techniques performed on molecules represented by 2D fingerprints. The major conclusion is that the high stability of adiabatically bound anions originates from the bonding character of the pi orbital occupied by the excess electron. This compensates for the antibonding character that usually causes significant buckling of the ring. Also, the excess electron is more homogenously distributed over both rings than in the case of anions of the most stable neutral species. In terms of 2D substructure, the most stable anionic tautomers generally have additional hydrogen atoms at C8 and/or C2 and they do not have hydrogen atoms attached to C4, C5, and C6. They also form an "island of stability" in the tautomeric space of guanine.     

Electronic structure of [(CpCr)[(CO)3M]]mu-Cot (M = Cr, Fe): a theoretical study

The electronic structure of two cyclooctatetraene-bridged dinuclear first-row transition metal complexes of the type [(CpM)[(CO)3M']]mu-Cot (M = Cr; M' = Fe (1), Cr (2)) was investigated by complete active space self-consistent field (CASSCF) calculations. In this context the differences in the binding capabilities of the complex fragments CpM and (CO)3M are discussed on the basis of extended Huckel molecular orbital (MO) calculations. The geometries used for the CASSCF calculations for complex 1 were obtained from the crystal structure. For 2 a model structure was established by geometry optimization using density functional methods. The CASSCF results agree well with the experimental findings and provide insight into the binding situation of the two compounds. Complex 1 can be regarded as being composed of a chromocene-like subunit CpCr(eta5-C5H5) and the fragment (CO)3Fe(eta3-C3H3). A direct metal-metal bond is found, involving one initially singly occupied orbital of each fragment, leading to a doublet ground state for 1 with the remaining unpaired electron localized at the chromium center. For 2 no such direct metal-metal bond can be recognized. A very weak direct metal-metal interaction is induced by electron donation from the Cot2- ligand into a formally unoccupied metal-metal binding orbital combination. In the quartet ground state all three unpaired electrons are localized at the chromium center of the formally doubly positive charged CpCr unit, on which complex fragment [(CO)3Cr(eta5-Cot)]2- acts like a cyclopentadienyl ligand. The coordination sphere of the chromium center of the CpCr unit resembles that of a metallocene metal center and its metal 3d occupation scheme corresponds to that of vanadocene.     

Quantum effect on the internal proton transfer and structural fluctuation in the H+ 5 cluster

The thermal equilibrium state of H+(5) is investigated by means of an ab initio path integral molecular dynamics (PIMD) method, in which degrees of freedom of both nuclei and electrons at finite temperature are quantized within the adiabatic approximation. The second-order Moller-Plesset force field has been employed for the present ab initio PIMD. At 5-200 K, H+(5) is shown to have the structure that the proton is surrounded by the two H(2) units without any exchange of an atom between the central proton and the H(2) unit. At 5 K, the quantum tunneling of the central proton occurs more easily when the distance between the two H(2) units is shortened. At the high temperature of 200 K, the central proton is more delocalized in space between the two H(2) units, with less correlation with the stretching of the distance between the two H(2) units. As for the rotation of the H(2) units around the C(2) axis of H+(5) , the dihedral angle distribution is homogeneous at all temperatures, suggesting that the two H(2) units freely rotate around the C(2) axis, while this quantum effect on the rotation of the H(2) units becomes more weakened with increasing temperature. The influence of the structural fluctuation of H+(5) on molecular orbital energies has been examined to conclude that the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap is largely reduced with the increase of temperature because of the spatial expansion of the whole cluster.     

Singlet–triplet splittings as obtained from the Xα-scattered wave method: A theoretical analysis

The theoretical determination of singlet–triplet splittings of the excited states of closed-shell molecules is discussed with emphasis on the use of the Xα–scattered wave method. With this method, splittings can be computed in two independent ways. Both will have corrections due to orbital relaxation effects. The singlet–triplet splittings obtained with the Xα–scattered wave method for several large organic molecules are reviewed. It is seen that the results using the two splitting formulas differ by a large amount; in fact, they differ by the magnitude of the computed splitting. We provide a criterion for choosing the results obtained with one method over the other by showing that they both give upper bounds to the best result obtainable within the framework of the model. However, because of the large differences between the two methods, the quantitative value of the splitting should be viewed with caution.     

Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (−)-menthyl acrylate revisited with the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method

The construction of the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method is detailed. This method is specifically devoted to the study of the reactivity of large chemical systems in solution. The solvent, modeled by a polarizable continuum, surrounds the whole solute molecule. Solute–solvent interactions are taken into account by means of the self-consistent reaction field approach. The solute system is treated by both quantum and molecular mechanics, the former being principally applied to the reactive part, i.e., the part undertaking bond forming or breaking, the latter being reserved for the ancillary encumbering groups. The connection between the molecular mechanics and the quantum mechanics part is accomplished by a strictly localized bond orbital that remains frozen within the local self-consistent field framework. As a test system, the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate is studied for the first time with steric interactions and electrostatic solvent effects taken into account simultaneously. The results indicate that the coupling of both interactions leads to conclusions that could not have been guessed from separate calculations.Proceedings of the 11th International Congress of Quantum chemistry satellite meeting in honour of Jean-Louis Rivail     

Mössbauer properties of the diferric cluster and the differential iron(II)-binding affinity of the iron sites in protein R2 of class Ia Escherichia coli ribonucleotide reductase: a DFT/electrostatics study

The R2 subunit of class-Ia ribonucleotide reductase (RNR) from Escherichia coli (E. coli) contains a diiron active site. Starting from the apo-protein and Fe(II) in solution at low Fe(II)/apoR2 ratios, mononuclear Fe(II) binding is observed indicating possible different Fe(II) binding affinities for the two alternative sites. Further, based on their M?ssbauer spectroscopy and two-iron-isotope reaction experiments, Bollinger et al. (J. Am. Chem. Soc., 1997, 119, 5976-5977) proposed that the site Fe1, which bonds to Asp84, should be associated with the higher observed (57)Fe M?ssbauer quadrupole splitting (2.41 mm s(-1)) and lower isomer shift (0.45 mm s(-1)) in the Fe(III)Fe(III) state, site Fe2, which is further from Tyr122, should have a greater affinity for Fe(II) binding than site Fe1, and Fe(IV) in the intermediate X state should reside at site Fe2. In this paper, using density functional theory (DFT) incorporated with the conductor-like screening (COSMO) solvation model and with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) methodologies, we have demonstrated that the observed large quadrupole splitting for the diferric state R2 does come from site Fe1(III) and it is mainly caused by the binding position of the carboxylate group of the Asp84 sidechain. Further, a series of active site clusters with mononuclear Fe(II) binding at either site Fe1 or Fe2 have been studied, which show that with a single dielectric medium outside the active site quantum region, there is no energetic preference for Fe(II) binding at one site over another. However, when including the explicit extended protein environment in the PB-SCRF model, the reaction field favors the Fe(II) binding at site Fe2 rather than at site Fe1 by ~9 kcal mol(-1). Therefore our calculations support the proposal of the previous M?ssbauer spectroscopy and two-iron-isotope reaction experiments by Bollinger et al.     

Interplay of Hückel and Möbius Aromaticity in Metal-Metal Quintuple Bonded Complexes of Cr,Mo, and W with Amidinate Ligand: Ab initio DFT and Multireference Analysis**

The aromaticity of metal-metal quintuple bonded complexes of the type M₂L₂ (M=Cr, Mo, and W; L=amidinate) are studied employing gauge including magnetically induced ring current (GIMIC) analysis and electron density of delocalized bonds (EDDB). It is found that the complexes possess two types of aromaticity: i) Hückel aromaticity through delocalization of ligand π electrons with metal-metal δ-bond-forming 6 conjugated electrons (4π and 2δ) ring; ii) Craig-Möbius aromaticity through delocalization of π electrons of both the ligands with metal d-orbitals in Craig type orientation forming 10π electrons ring with a double twist. Extended transition state natural orbital chemical valence (ETS-NOCV) and canonical molecular orbital natural chemical shielding (CMO-NCS) analysis confirm the Craig-Möbius type arrangement of the orbitals. Furthermore, the unprecedented Hückel and Möbius type aromaticity is confirmed from the plot of the current pathways using 3D line integral convolution (3D-LIC) plots. The metal-metal bond order also increases down the group as justified from the complete active space self-consistent field (CASSCF) analysis. Due to an increase in the π and δ electron conjugation, both the Hückel and Möbius aromaticity increase down the group.     

Photochemical inactivation of trypsin

Abstract —The quantum yield for inactivation of aqueous trypsin fits the expression φ_f=Σ_rf_rφ‘_r, where f_r, is the fraction of incident light absorbed by residues of type r and the φ’_r are constants. The values φ‘_trp= 0.012, φ_tyr= 0.005 and φ’_eys= 0.10, obtained at pH 3 in the wavelength range 240–290 nm, are attributed to independent events by comparing with quantum yields of the initial photochemical products and permanent residue destruction. The proposed inactivating processes are photoionization of one essential tryptophyl residue, photolysis of one essential cystyl residue, and splitting of an essential cystyl residue induced by light absorption in a nearby tyrosyl residue. The initial photochemical process from pH 3–7 identified by flash photolysis is the ejection of electrons from approximately two tryptophyl residues, leading to the formation of the disulfide bridge electron adduct and the hydrated electron. It is proposed that one photoionized tryptophyl residue is permanently disrupted and the other is restored through a back reaction that leads to a damaged, active enzyme form. An enhanced inactivation quantum yield at flash photolysis light intensities is attributed to a biphotonic process. A model based on one-photon photoionization of tryptophan from a short-lived precursor of the fluorescent state and the biphotonic photoionization of tryptophan via the triplet state is consistent with the experimental results.     

氟硼二吡咯类pH荧光探针PET光谱特性的理论计算

氟硼二吡咯(BODIPY)类pH荧光探针分子是基于光诱导电子转移(PET)的荧光探针分子, 识别基团氮原子上引入不同取代基可呈现不同的光学灵敏度. 本文应用密度泛函理论(DFT)及含时密度泛函理论(TD-DFT)方法对六种含不同取代基的探针分子进行了几何构型优化及激发态计算, 探讨了不同取代基对PET效应影响. 计算结果表明: 基态时这些探针分子的最高占有分子轨道(HOMO)和最低未占有分子轨道(LUMO)都在荧光母体BODIPY的π, π^*轨道, 而识别基团上氮原子孤对电子所在的轨道为HOMO-1轨道. 但是在激发态, 当氮原子上有两个取代基时, HOMO-1→LUMO跃迁的激发能都小于荧光团的HOMO→LUMO跃迁, 这将有可能产生PET效应并导致荧光熄灭, 而当氮原子上有一个取代基时不会出现这种现象. 通过激发态结构优化可以发现, 无论识别基团氮原子上有一个还是两个取代基, N原子的轨道对称性都发生变化, 由sp³→sp², 孤对电子占据在p轨道上, 其轨道能级升高至荧光团的HOMO和LUMO轨道之间, 将导致不同程度的PET效应, 与实验结果一致.