Inner-sphere electron-transfer reorganization energies of zinc porphyrins

Inner-sphere electron-transfer reorganization energies of Zn(protoporphyrin IX) and Zn(octaethylporphyrin) are determined from band-shape analyses of the first ionization obtained by gas-phase valence photoelectron spectroscopy. The experimentally determined total inner-sphere reorganization energies for self-exchange (120-140 meV) indicate that structural changes upon oxidation are largely confined to the porphyrin ring, and substituents on the ring or solvent and other environmental factors make smaller contributions. Computational estimates by different models vary over a wide range and are sensitive to numerical precision factors for these low reorganization energies. Of current computational models that are widely available and practical for molecules of this size, functionals that contain a mixture of Hartree-Fock exchange and DFT exchange-correlation appear to be the most applicable.     

Reaction mechanism of porphyrin metallation studied by theoretical methods

We have studied the reaction mechanism for the insertion of Mg2+ and Fe2+ into a porphyrin ring with density functional calculations with large basis set and including solvation, zero-point and thermal effects. We have followed the reaction from the outer-sphere complex, in which the metal is coordinated with six water molecules and the porphyrin is doubly protonated, until the metal ion is inserted into the deprotonated porphyrin ring with only one water ligand remaining. This reaction involves the stepwise displacement of five water molecules and the removal of two protons from the porphyrin ring. In addition, a step seems to be necessary in which a porphyrin pyrrolenine nitrogen atom changes its interaction from a hydrogen bond to a metal-bound solvent molecule to a direct coordination to the metal ion. If the protons are taken up by a neutral imidazole molecule, the deprotonation reactions are exothermic with minimal barriers. However, with a water molecule as an acceptor, they are endothermic. The ligand exchange reactions were approximately thermoneutral (+/-20 kJ mol(-1), with one exception) with barriers of up to 72 kJ mol(-1) for Mg and 51 kJ mol(-1) for Fe. For Mg, the highest barrier was found for the formation of the first bond to the porphyrin ring. For Fe, a higher barrier was found for the formation of the second bond to the porphyrin ring, but this barrier is probably lower in solution. No evidence was found for an initial pre-equilibrium between a planar and a distorted porphyrin ring. Instead, the porphyrin becomes more and more distorted as the number of metal-porphyrin bonds increase (by up to 191 kJ mol(-1)). This strain is released when the porphyrin becomes deprotonated and the metal moves into the ring plane. Implications of these findings for the chelatase enzymes are discussed.     

Reactivities and biological functions of iron-sulfur clusters

Iron-sulfur clusters are prevalent in biological systems. Through studies of iron-sulfur proteins and synthetic model clusters, it was realized early on that these clusters functioned as facile electron transfer agents. Until recently it was widely thought that they served exclusively in that capacity. However, in the last decade, it has become clear that their reactivities and biological functions are much more diverse. It is now apparent that these clusters can serve as the active sites of enzymes, as well as in the regulation of enzymatic activity. Synthetic clusters, which have been shown to undergo a variety of core rearrangements or structural changes, have provided insight into possible mechanisms of cluster formation or activity regulation in enzymes. Rigid tripodal ligands have been constructed which capture synthetic iron-sulfur clusters in a cavity which permits controlled reactivity studies. In this article, we review these recent developments and suggest some future directions the field may take.     

On the accuracy of density functional theory for iron-sulfur clusters

A simple, yet powerful wave function manipulation method was introduced utilizing a generalized ionic fragment approach that allows for systematic mapping of the wave function space for multispin systems with antiferromagnetic coupling. The use of this method was demonstrated for developing ground state electronic wave function for [2Fe-2S] and [Mo-3Fe-4S] clusters. Using well-defined ionic wave functions for ferrous and ferric irons, sulfide, and thiolate fragments, the accuracy of various density functionals and basis sets including effective core potentials were evaluated on a [4Fe-4S] cluster by comparing the calculated geometric and electronic structures with crystallographic data and experimental atomic spin densities from X-ray absorption spectroscopy, respectively. We found that the most reasonable agreement for both geometry and atomic spin densities is obtained by a hybrid functional with 5% HF exchange and 95% density functional exchange supplemented with Perdew's 1986 correlation functional. The basis set seems to saturate only at the triple-zeta level with polarization and diffuse functions. Reasonably preoptimized structures can be obtained by employing computationally less expensive effective core potentials, such as the Stuttgart-Dresden potential with a triple-zeta valence basis set. The extension of the described calibration methodology to other biologically important and more complex iron-sulfur clusters, such as hydrogenase H-cluster and nitrogenase FeMo-co will follow.     

Fourfold clusters of rovibrational energies in H2Te studied with an ab initio potential energy function

We report here an ab initio investigation of the cluster effect (i.e., the formation of four-member groups of nearly degenerate rotation-vibration energy levels at higher J and K_a values) in the H₂Te molecule. The potential energy function has been calculated ab initio at a total of 334 molecular geometries by means of the CCSD (T) method where the (1s-4f) core electrons of the Te atom were described by an effective core potential. The values of the potential energy function obtained cover the region up to around 10 000 cm⁻¹ above the equilibrium energy. On the basis of the ab initio potential, the rotation-vibration energy spectra of H₂ ¹³⁰Te and its deuterated isotopomers have been calculated with the MORBID (Morse oscillator rigid bender internal dynamics) Hamiltonian and computer program. In particular, we have calculated the rotational energy manifolds for J40 in the vibrational ground state, the ν₂ state, the “first triad” (the ν₁/ν₃/2 ν₂ interacting vibrational states), and the “second triad” (the (ν₁ + ν₂)/(ν₂ + ν₃)/3 ν₂ states) of H₂¹³⁰Te. We have also investigated the cluster formation in the vibrational ground state of H₂ ¹³⁰Te by first fitting the rotational data available from experiment with a modified Watson-type effective Hamiltonian and then using the optimized ground state constants to extrapolate the rotational structure to higher J values. Both the ab initio calculation and the prediction with the effective Hamiltonian show that the cluster formation in H₂Te is very similar to that in H₂Se and H₂S, which we have studied previously. However, contrary to semiclassical predictions, we do not determine any significant displacement of the clusters towards lower J values relative to H₂Se. Hence the experimental observation of the cluster states in H₂Te will be at least as difficult as in H₂Se.     

Hydrogen-bonded clusters of hydroperoxyl radical with ammonia: a theoretical study

Ab initio calculations at MP2/6-311++G(d,p) computational level were used to analyze the interaction between a molecule of the hydroperoxyl radical with 1 up to 4 molecules of ammonia. Three minima were found for 1:2 and 1:4 complexes of HOO and NH₃. Two complexes were located as minima on the potential energy surface of 1:3 complexes. Red shifts of the OH stretching frequency upon complex formation in the range between 560 and 1,116 cm⁻¹ are predicted. Cooperative effect in terms of stabilization energy is calculated for the studied clusters. The cooperative effect is increased with the increasing size of studied clusters. The Quantum Theory Atoms in Molecules (QTAIM) theory was also applied to explain the nature of the complexes.     

Formation and bonding of alane clusters on Al(111) surfaces studied by infrared absorption spectroscopy and theoretical modeling

Alanes are believed to be the mass transport intermediate in many hydrogen storage reactions and thus important for understanding rehydrogenation kinetics for alanates and AlH3. Combining density functional theory (DFT) and surface infrared (IR) spectroscopy, we provide atomistic details about the formation of alanes on the Al(111) surface, a model environment for the rehydrogenation reactions. At low coverage, DFT predicts a 2-fold bridge site adsorption for atomic hydrogen at 1150 cm(-1), which is too weak to be detected by IR but was previously observed in electron energy loss spectroscopy. At higher coverage, steps are the most favorable adsorption sites for atomic H adsorption, and it is likely that the AlH3 molecules form (initially strongly bound to steps) at saturation. With increasing exposures AlH3 is extracted from the step edge and becomes highly mobile on the terraces in a weakly bound state, accounting for step etching observed in previous STM studies. The mobility of these weakly bound AlH3 molecules is the key factor leading to the growth of larger alanes through AlH3 oligomerization. The subsequent decomposition and desorption of alanes is also investigated and compared to previous temperature programmed desorption studies.     

物理法COD减排理论极限能耗的热力学分析

首先针对系统的可持续性发展提出了三点本质要求,在此基础上提出了基于减排过程节能机制的热力学框架,并根据热力学第一、第二定律建立了计算物理法脱除有机污染物理论极限能耗的热力学分析方法.此外,以典型有机污染物的脱除为例,分别计算了封闭体系中298.15K和1.01325×105Pa下不同初始浓度、不同种类以及不同COD减排量的有机污染物脱除的理论极限能耗.本文的计算结果表明,废水中有机污染物的减排需要很高的能耗,脱除相同量有机污染物所需的理论极限能耗随着初始浓度的减小而显著增加,且不同种类污染物处理的难易程度和能耗高低相差很大,这充分说明减排与节能有着密不可分的联系,充分考虑污染物的种类、物理化学性质、毒性和浓度将有助于减排政策的科学制定.     

Photoionization of epichlorohydrin enantiomers and clusters studied with circularly polarized vacuum ultraviolet radiation

The photoionization of enantiomerically pure epichlorohydrin (C(3)H(5)OCl) has been studied using linearly and circularly polarized vacuum ultraviolet synchrotron radiation. The threshold photoelectron spectrum was recorded and the first three bands assigned using molecular orbital calculations for the expected conformers, although uncertain experimental conformer populations and an anticipated breakdown in Koopmans' theorem leave some ambiguity. Measurements of the photoelectron circular dichroism (PECD) were obtained across a range of photon energies for each of these bands, using electron velocity map imaging to record the angular distributions, during which a record PECD chiral asymmetry factor of 32% was observed. A comparison with calculated PECD curves clarifies the assignment achieved using ionization energies alone and further suggests a likely relative population of the conformers. Threshold photoelectron-photoion coincidence methods were used to study the ionic fragmentation of epichlorohydrin. Fragment ion appearance energies show nonstatistical behavior with clear indications that the cationic epoxide ring is unstable and lower energy decay channels proceeding via ring breaking are generally open. Extensive neutral homochiral clusters of epichlorohydrin may be formed in supersonic molecular beam expansions seeded in Ar. Electron angular distribution measurements made in coincidence with dimer and trimer ions are used to effect an examination of the PECD associated with ionization of size-selected neutral cluster species, and these results differ clearly from PECD of the neutral monomer. The shifted ionization thresholds of the n-mers (n = 2, ..., 7) are shown to follow a simple linear relationship, but under intense beam expansion conditions the monomer deviates from this relationship, and the monomer electron spectra tail to below the expected monomer adiabatic ionization potential (IP). PECD measurements made in coincidence with monomer ions obtained under different beam expansion conditions were used to identify unambiguously a contribution from dissociative photoionization of larger clusters to the monomer parent mass ion yield above and below its adiabatic IP.     

Geometry, reduction potential, and reorganization energy of the binuclear Cu(A) site, studied by density functional theory

The dimeric Cu(A) site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the structure of the realistic (Im)(S(CH(3))(2))Cu(SCH(3))(2)Cu(Im)(CH(3)CONHCH(3)) model in the fully reduced, mixed-valence, and fully oxidized states. The optimized structures are very similar to crystal structures of the protein, which shows that the protein does not strain the site significantly. Instead, inorganic model complexes of the protein site are strained by the macrocyclic connections between the ligand models. For the mixed-valence (Cu(I)+Cu(II)) state, two distinct equilibrium structures were found, one with a short Cu-Cu distance, 248 pm, similar to the protein structure, and one with a longer distance, 310 pm, similar to what is found in inorganic models. In the first state, the unpaired electron is delocalized over both copper ions, whereas in the latter, it is more localized to one of the ions. The two states are nearly degenerate. The potential energy surfaces for the Cu-Cu, Cu-S(Met), and Cu-O interactions are extremely flat. In fact, all three distances can be varied between 230 and 310 pm at an expense in energy of less than 8 kJ/mol, which explains the large variation observed in crystal structures for these interactions. Inclusion of solvation effects does not change this significantly. Therefore, we can conclude that a variation in these distances can change the reduction potential of the Cu(A) site by at most 100 mV. The model complex has a reorganization energy of 43 kJ/mol, 20 kJ/mol lower than for a monomeric blue-copper site. This lowering is caused by the delocalization of the unpaired electron in the mixed-valence state.     

Potential energy surfaces of sodium clusters

We have calculated multidimensional Born- Oppenheimer energy surfaces of singly charged and neutral sodium clusters with quadrupole, octupole, and hexadecapole deformed shapes in a particle range from 8 ≤ N ≤ 58. We use the local-density approximation (LDA) and solve the Kohn-Sham equations on a cylindrical mesh for axially symmetric shapes. Employing the structure-averaged jellium model (SAJM), we ascertain that the correct empirical bulk properties and surface tension are reproduced. Besides a pronounced isomerism in the β ₂/β ₄ plane we also find super-deformed shapes. We compare the PES data with shape transitions deduced from experimental splittings of the dipole. photoabsorption cross sections. The influence of large octupole moments reverts the scheme of prolate-oblate shape transitions above the filled 2p-shell (N = 42, 44) which is wrongly predicted in spheroidal models.     

Solvent reorganization energy of electron-transfer reactions in polar solvents

A microscopic theory of solvent reorganization energy in polar molecular solvents is developed. The theory represents the solvent response as a combination of the density and polarization fluctuations of the solvent given in terms of the density and polarization structure factors. A fully analytical formulation of the theory is provided for a solute of arbitrary shape with an arbitrary distribution of charge. A good agreement between the analytical procedure and the results of Monte Carlo simulations of model systems is achieved. The reorganization energy splits into the contributions from density fluctuations and polarization fluctuations. The polarization part is dominated by longitudinal polarization response. The density part is inversely proportional to temperature. The dependence of the solvent reorganization energy on the solvent dipole moment and refractive index is discussed.     

Thermodynamic analysis of the theoretical energy consumption in the removal of organic contaminants by physical methods

The essential requirements for evaluating the sustainable development of a system and the thermodynamic framework of the energy conservation mechanism in the waste-removal process are proposed.A thermodynamic method of analysis based on the first and second laws of thermodynamics is suggested as a means to analyze the theoretical energy consumption for the removal of organic contaminants by physical methods.Moreover,the theoretical energy consumption for the removal by physical methods of different kinds of...     

Structure reorganization dynamics of water clusters upon vertical ionization: Quantum chemical investigation

Quantum dynamics simulations of (H₂O) _n ⁺ water cluster cations comprising up to six molecules with the initial configurations of stable neutral isomers are combined with stationary calculations of the same cations in order to get nonempirical information about water cluster relaxation after the absorption of energy in a range of from 11.0 to 12.0 eV. The electronic problem was solved and the potential energy of the system was estimated in terms of the restricted or unrestricted Hartree-Fock approximation with the 6–31++G** atomic basis set taking into account second-order Möller-Plesset perturbation theory corrections. Calculations of dynamic trajectories were based on the Born-Oppenheimer approximation. The formation of stable water cluster cations is shown to be a multistage process, the principal stages of which are qualitatively correctly reflected by the sequence of steps in cation geometry optimization runs.     

Interfacial reactivity of monolayer-protected clusters studied by scanning electrochemical microscopy

Solutions of monodisperse monolayer-protected clusters (MPCs) of gold can be used as multivalent redox mediators in electrochemical experiments due to their quantized double-layer charging properties. We demonstrate their use in scanning electrochemical microscopy (SECM) experiments wherein the species of interest (up to 2-electron reduction or 4-electron oxidation from the native charge-state of the MPCs) is generated at the tip electrode, providing a simple means to adjust the driving force of the electron transfer (ET). Approach curves to perfectly insulating (Teflon) and conducting (Pt) substrates are obtained. Subsequently, heterogeneous ET between MPCs in 1,2-dichloroethane and an aqueous redox couple (Ce(IV), Fe(CN)63-/4-, Ru(NH3)63+, and Ru(CN)64-) is probed with both feedback and potentiometric mode of SECM operation. Depending on the charge-state of the MPCs, they can accept/donate charge heterogeneously at the liquid-liquid interface. However, this reaction is very slow in contrast to ET involving MPCs at the metal-electrolyte interface.     

铁硫蛋白活性中心铁硫簇的对称性破缺密度泛函 计算

应用密度泛函方法(DFT)计算了铁硫金属蛋白中的铁硫簇[Fe~2S~2(SCH~3)~4]^2^-,[Fe~3S~4(SCH~3)~3]^2^-以及[Fe~4S~4(SCH~3)~4]^2^-的几何参数和磁偶合性质。采用对称性破缺态(BS)来描述Fe－Fe自旋偶合。计算结果表明：采用高自旋态(HS)计算的Fe－Fe间距与实验值有较大偏差,而由BS方法所计算的Fe－Fe间距与晶体结构测定数据相吻合。根据HS态和BS态的能量,计算了体系的海森堡偶合参数J,计算结果也较为接近实验估算值。     

Dissociative recombination of ammonia clusters studied by storage ring experiments

Dissociative recombination of ammonia cluster ions with free electrons has been studied at the heavy-ion storage ring CRYRING (Manne Siegbahn Laboratory, Stockholm University). The absolute cross sections for dissociative recombination of H+(NH3)2, H+(NH3)3, D+(ND3)2, and D+(ND3)3 in the collision energy range of 0.001-27 eV are reported, and thermal rate coefficients for the temperature interval from 10 to 1000 K are calculated from the experimental data and compared with earlier results. The fragmentation patterns for the two ions H+(NH3)2 and D+(ND3)2 show no clear isotope effect. Dissociative recombination of X+(NX3)2 (X=H or D) is dominated by the product channels 2NX3+X [0.95+/-0.02 for H+(NH3)2 and 1.00+/-0.02 for D+(ND3)2]. Dissociative recombination of D+(ND3)3 is dominated by the channels yielding three N-containing fragments (0.95+/-0.05).     

Dipole excitation of Na clusters with a non-local energy density functional

The elementary dipole excitations of the ionized clusters Na ₉ ⁺ , Na ₂₁ ⁺ and Na ₄₁ ⁺ are investigated by solving the equations of the Random-Phase Approximation. The ground and excited states are described using the jellium model for the ionic background and a non-local energy density functional for the valence electrons. Non-local effects are specifically analyzed. The excitation energies thus obtained approach better than those of the Local Density Approximation both the full Hartree-Fock and the experimental results.