Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.     

Quantum Monte Carlo Calculation of Correlation Effects on Bond Orders

We present a computational approach, using quantum Monte Carlo, that provides some insight into the effect of electron correlation on chemical bonding between individual pairs of atoms. Our approach rests upon a recently suggested relation between the bond order and charge fluctuations with respect to atomic domains. Within the present implementation we have taken a compromise between conceptual rigour and computational simplicity. In a first step atomic domains were obtained from Hartree-Fock (HF) densities, using Bader’s definition of atoms in molecules. These domains were used in a second step in quantum Monte Carlo calculations to determine bond orders for pairs of atoms. Correlation effects have been studied by comparison of HF bond orders with those obtained from pure diffusion quantum Monte Carlo calculations. We illustrate this concept for C–O and C–S bonds in different molecular environments. Our results suggest an approximate linear relation between bond order and bond length for these kinds of bonds.     

Molecule‐specific determination of atomic polarizabilities with the polarizable atomic multipole model

Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near‐quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability. © 2012 Wiley Periodicals, Inc.     

An experimental look into subelectron charge flow

The prediction and measurement of charge distribution among interacting chemical entities in complex environments is a major challenge for modern chemistry. It encompasses information concerning fundamental quantities such as the electronic chemical potential and hardness of molecular fragments as well as their interactions with the surroundings. Although a wealth of theoretical work has been accumulated from the days of Pauling to the present, a specific molecular model system that allows quantitative and direct measurement of these properties has not yet been reported. Because atomic charges are not quantum mechanical observables, they cannot be derived from first principles, but rather they rely on the availability of high-precision experimental data and the interpretation of related experimental observables. Here, we demonstrate, for the first time, that a fragmental charge flow between a chelated metal center and reversibly bound molecules can be accurately monitored experimentally.     

Assessment of quantum‐chemical methods for electronic properties and geometry of signaling biomolecules

A reasonable balance between accuracy and feasibility of quantum‐chemical methods depends on the complexity of the molecular system and the scientific goals. Six series of indole‐, naphthalene‐, phenol‐, benzoic‐, phenoxy‐, other auxin‐derivatives, and a test set of similar organic molecules have been chosen for an assessment of 13 density functional and semi‐empirical molecular orbital methods with respect to electronic and structural properties. The accuracy and precision of HOMO/LUMO calculations are determined by comparison with experimental ionization potentials and electron affinities. Further comparison was performed at atomic level by covariance analysis. The methods KMLYP, MSINDO, and PM3 are precise and accurate for the whole set of molecules. The method AM1 offers comparable accuracy with the exception of electron affinities of indole derivatives, where significant deviations from experiment were observed. Geometrical properties were best reproduced with the semi‐empirical method MSINDO. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

The any particle molecular orbital approach: A short review of the theory and applications

The any particle molecular orbital (APMO) approach extends regular electronic structure methods to study atomic and molecular systems in which electrons and other particles are treated simultaneously as quantum waves. A number of electronic structure methodologies have been extended under the APMO framework and applied to investigate nuclear quantum effects including isotope effects and nuclear delocalization and to calculate proton binding energies and affinities. In addition, APMO methodologies have been employed to analyze physical and chemical properties of atomic and molecular systems containing exotic subatomic particles.     

层状双金属氢氧化物微观结构与性质的理论研究进展

总结了近年来理论计算方法在研究层状双金属氢氧化物(LDHs)结构与功能方面的应用现状. 结合LDHs材料的结构特点, 归纳了量子力学、分子力学、几何建模及物理静电模型相结合对LDHs材料进行结构模拟的思路, 比较了各种方法在LDHs结构模拟上的优势及存在的不足. 量子力学方法能够精确获得水滑石材料的层板构成及作用机制、简单阴离子插层水滑石主客体间的超分子作用实质以及电子性质、反应机理等方面的信息. 与量子力学相比较, 分子力学方法可以快速得到插层水滑石材料的层间阴离子排布及取向、水合膨胀特性及宏观力学性质等. 几何模型和物理静电模型能构建直观、形象的数学模型, 大大简化了计算量,因此能计算接近实际LDHs尺寸的体系, 为推测LDHs结构信息提供了可能性. 随着理论方法和计算机硬件水平的发展, 使得计算机模拟技术逐渐成为获得LDHs材料微观结构参数、电子性质和动力学性质的一种有效手段.     

Synergy between theory and experiment in structure resolution of low-dimensional oxides

In this paper, I review recent progress in joint theoretical and experimental studies aiming at atomic structure determination of low-dimensional metal oxides. Low-dimensional systems can be generally defined as materials of unusual structure that extend to less than three dimensions. In recent years low-dimensional systems have attracted increasing attention of physicists and chemists, and the interest is expected to rise in the near future. Two- and one-dimensional structures in form of thin oxide films or elongated oxide chains have many potential applications including model supports for heterogeneous catalysts and insulating layers in semiconductor industry. The interest in zero-dimensional gas-phase oxide clusters ranges from astrophysics to studies of elementary steps in catalysis. The key prerequisite for understanding physical and chemical properties of low-dimensional systems is a detailed knowledge of their atomic structures. However, such systems frequently present complex structures to solve. Only in a few cases experimental data can provide some information about possible arrangement of atoms, but data interpretation relies to a large extent on intuition. Therefore, in the recent years quantum chemical calculations became an indispensable tool in structure identification of low-dimensional systems, yet the accuracy of theoretical tools is often limited. The results reviewed here demonstrate that often the only way of an unambiguous atomic structure determination of low-dimensional systems are experimental studies combined with theoretical calculations. Particularly the global optimization methods such as genetic algorithm in combination with the density functional theory prove very useful in automatic structure determination of the observed surface structures and gas-phase clusters.     

有机二硫化物润滑添加剂抗磨极压性能的密度泛函理论研究

用量子化学的密度泛函理论计算了12种有机二硫化物和铁原子簇的分子轨道指数及其与铁原子簇的化学吸附作用能, 探讨了这种作用能与抗磨性能的关系; 运用轨道能量近似原则讨论了有机二硫化物与铁原子的作用方式; 以前线电子密度、超离域性指数和原子净电荷作为判据分析了12种有机二硫化物与铁原子间键合的强弱、反应性的大小等表征有机二硫化物与金属作用强弱的参数。结果表明: 有机二硫化物与铁接触时, 在较缓和条件下, SS键优先断裂与金属发生化学吸附形成配位键, 起到抗磨作用; 在高负荷下, 与金属发生常规条件下不能发生的化学反应, 即CS键断裂生成无机膜, 起到极压作用; 且随着碳链的增长, 有机二硫化物的抗磨性能愈来愈好, 但极压性能愈来愈差; 运用量子化学计算得到的预测结果与摩擦学试验结果具有良好的一致性, 可为同类极压添加剂化合物的分子设计提供较为可靠的参考依据和理论方法。     

Single-molecule force spectroscopy measurements of bond elongation during a bimolecular reaction

It is experimentally challenging to directly obtain structural information of the transition state (TS), the high-energy bottleneck en route from reactants to products, for solution-phase reactions. Here, we use single-molecule experiments as well as high-level quantum chemical calculations to probe the TS of disulfide bond reduction, a bimolecular nucleophilic substitution (S N2) reaction. We use an atomic force microscope in force-clamp mode to apply mechanical forces to a protein disulfide bond and obtain force-dependent rate constants of the disulfide bond reduction initiated by a variety of nucleophiles. We measure distances to the TS or bond elongation (Delta x), along a 1-D reaction coordinate imposed by mechanical force, of 0.31 +/- 0.05 and 0.44 +/- 0.03 A for thiol-initiated and phosphine-initiated disulfide bond reductions, respectively. These results are in agreement with quantum chemical calculations, which show that the disulfide bond at the TS is longer in phosphine-initiated reduction than in thiol-initiated reduction. We also investigate the effect of solvent environment on the TS geometry by incorporating glycerol into the aqueous solution. In this case, the Delta x value for the phosphine-initiated reduction is decreased to 0.28 +/- 0.04 A whereas it remains unchanged for thiol-initiated reduction, providing a direct test of theoretical calculations of the role of solvent molecules in the reduction TS of an S N2 reaction. These results demonstrate that single-molecule force spectroscopy represents a novel experimental tool to study mechanochemistry and directly probe the sub-?ngstr?m changes in TS structure of solution-phase reactions. Furthermore, this single-molecule method opens new doors to gain molecular level understanding of chemical reactivity when combined with quantum chemical calculations.     

MOLCAS 7: The Next Generation

Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two‐electron integrals and in the generation of so‐called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self‐consistent field, density functional theory, 2nd order perturbation theory, complete‐active space self‐consistent field multiconfigurational reference 2nd order perturbation theory, and coupled‐cluster methods. The report further elaborates on the implementation of a restricted‐active space self‐consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas‐Kroll‐Hess transformation for one‐component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so‐called picture‐change‐free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

最小二乘支持向量机方法用于提高低水平量子化学方法计算吸收能的精度

运用B3LYP/STO-3G和ZINDO两种低水平的量子化学方法计算了160个有机分子的UV-Vis吸收光谱, 然后提取合适的物理参数, 并以实验值为基础, 引入最小二乘支持向量机方法以提高吸收能的计算值精度. 结果表明, 最小二乘支持向量机方法可有效提高量子化学计算精度, 体系的吸收能误差均方根分别从0.95和0.46 eV降低到0.16和0.15 eV. 最小二乘支持向量机校正方法的引入可在较少的机时和计算资源下得到比单一的量子化学计算方法更为稳定和精确的计算结果, 且可在现有计算条件下预测现有计算能力达不到的精度. 因此, 将最小二乘支持向量机方法用于量子化学数据分析, 为化学研究准确、 快捷地预测分子性质提供了一种新的研究手段.     

Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry

The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.