The Real and the VIrtual：Learning with COmputer Supported Microchemistry

Most science educators say that practical work is an essential part of science education.As regards chemistry,a recent IUPAC reprot endorses this …education in chemstry must have an ineluctable experimental component”。     

Do spin state changes matter in organometallic chemistry? A computational study

Spin changes occur often in organometallic chemistry, and their effect on kinetics is not well understood. We report computations on the singlet and triplet potential energy surfaces of several processes of this type and show that the topology of the individual surfaces, as well as of the crossing regions between them, can be used to rationalize the observed reactivity in all cases. In particular, the slow addition of dihydrogen to W[N(CH(2)CH(2)NSiMe(3))(3)]H (Schrock, R. R.; Shih, K. Y.; Dobbs, D. A.; Davis, W. M. J. Am. Chem. Soc. 1995, 117, 6609) is shown to be a "spin-blocked" reaction with a high barrier due to the crossing between reactant triplet and product singlet surfaces. In contrast, addition of CO to TpCo(CO) (Detrich, J. L.; Reinaud, O. M.; Rheingold, A. L.; Theopold, K. H. J. Am. Chem. Soc. 1995, 117, 11745) is fast because the triplet and singlet surfaces cross at low energy. Particular care is taken to use DFT methods which are in adequate agreement with experimental and high-level computational energetics for these systems.     

Evaluation of data for atmospheric models: master equation/RRKM calculations on the combination reaction, BrO + NO2 --> BrONO2, a conundrum

Experimental data for the title reaction were modeled using master equation (ME)/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA (Sander, S. P.; Finlayson-Pitts, B. J.; Friedl, R. R.; Golden, D. M.; Huie, R. E.; Kolb, C. E.; Kurylo, M. J.; Molina, M. J.; Moortgat, G. K.; Orkin, V. L.; Ravishankara, A. R. Chemical Kinetics and Photochemical Data for Use in Atmospheric Studies, Evaluation Number 15; Jet Propulsion Laboratory: Pasadena, California, 2006)1 and IUPAC (Atkinson, R.; Baulch, D. L.; Cox, R. A.; R. F. Hampson, J.; Kerr, J. A.; Rossi, M. J.; Troe, J. J. Phys. Chem. Ref. Data 2000, 29, 167)2 data evaluation panels, which represents the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies (Parthiban, S.; Lee, T. J. J. Chem. Phys. 2000, 113, 145)3 and a value (Orlando, J. J.; Tyndall, G. S. J. Phys. Chem. 1996, 100, 19398)4 of the bond dissociation energy, D298(BrO-NO2) = 118 kJ mol-1, corresponding to DeltaH0o = 114.3 kJ mol-1 at 0 K) and the use of RRKM/ME methods, fitting calculations to the reported data or the empirical equations was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca. 4 at, or close to, the low-pressure limit. Agreement between calculation and experiment could be achieved in two ways, either by increasing DeltaH0o to an unrealistically high value (149.3 kJ mol-1) or by increasing DeltaEd, the average energy transferred in a downward collision, to an unusually large value (>5000 cm-1). The discrepancy could also be reduced by making all overall rotations fully active. The system was relatively insensitive to changing the moments of inertia in the transition state to increase the centrifugal effect. The possibility of involvement of BrOONO was tested and cannot account for the difficulties of fitting the data.     

计算化学实验的课程建设

With the fast development of theoretical chemistry methodologies and computer hardware and software technologies, computational chemistry has become more and more imperative in chemical science. Accordingly, we have initiated "Computational Chemistry Experiments" course based on "Introductory Computational Chemistry" course developed in the Department of Chemistry, Tsinghua University since 2013, to provide basic training and computational chemistry practices for undergraduate students. The popular quantum chemistry software Gaussian is used as the major tool in the course. We focus on the exploratory feature of computational chemistry, creating initial structures and optimizing geometries, to provide fundamental training for students to comprehend the difference of traditional experimental chemistry and modern computational chemistry. Systematic research training is offered to develop the creative thinking capacity of students in using computational chemistry methods in chemistry education and research.     

Special Collection: Computational Chemistry

Chemists know well the value of an experimental or a theoretical result, but what is the value of a computational result? Simulation is neither theory nor experience, nor a mere calculation tool, but a genuine way of approaching reality that is transforming the scientific method. In some cases, it offers explanations to observations or experiments that seem incomprehensible because they are too complex. In this case, the computation serves as a relief. An experiment that converges with a certain computation has more scientific value than an experiment that does not converge with anything at all. In other cases, contribution of computational chemistry is essential because there is no experimental manner to determine what happens during a chemical process; for instance, in the path from reactants to products in (fast) reactions. Now, computational chemistry provides additional information that is not possible to obtain from experiments, so it is a valuable complement to them. Indeed, fruitful synergy between computation and experiment has led to the approach of theory-driven experimentation. Finally, computational chemistry helps to legitimize models or theories that have little opportunity to be contrasted with reality. In this situation, computational chemistry is not experience, but it does substitute it in relation to theory. In the present special collection, we have examples of the different ways computational chemistry helps chemists to interpret the electronic and molecular structure of molecules and their reactivity.     

Computational Chemistry techniques: covering orders of magnitude in space, time, and accuracy

Computational Chemistry is the branch of chemistry which uses extensively computer models to simulate real systems. Model systems are made to fit the real system in intended respects and with the intended accuracy of the creator or user of the model. The building blocks of model systems and the interactions between them are abstractions of the building blocks of real system and the interactions between them. In computer models a system must be represented by data which are stored in data structures, the interactions between them are represented by mathematical functions or sets of rules. Properties of the model system are calculated with various algorithms, both numerical and non-numerical. A computational chemist must decide which computer model is best suited to represent a real system so that its essential properties can be simulated as intended. Doing computational chemistry means to apply the right computer models to describe a real system or, if necessary, design new computer models.     

Cross-docking of inhibitors into CDK2 structures. 1

Predicting protein/ligand binding affinity is one of the most challenging computational chemistry tasks. Numerous methods have been developed to address this challenge, but they all have limitations. Failure to account for protein flexibility has been a shortcoming of many methods. In this cross-docking study the data set comprised 150 inhibitor complexes of the protein kinase CDK2. Gold and Glide performed well in terms of docking accuracy. The chance of cross-docking a ligand within a 2 A RMSD of its experimental pose was found to be 50%. Relative binding potency was not properly predicted from scoring functions, even though cross-docking of each inhibitor into each protein structure was performed and only scores of correctly docked ligands were considered. An accompanying paper (Voigt, J. H.; Elkin, C.; Madison, V. S. Duca, J. S. J. Chem. Inf. Model. 2008, 48, 669-678) covers cross-docking and docking accuracy from the perspective of using multiple protein structures.     

Uses of pH electrodes in nuclear chemistry

The determination and definition of pH is a controversial subject in many areas in chemistry. For these reasons the International Union of Pure and Applied Chemistry (IUPAC) has developed recommendations for pH measurement. These recommendations are currently (winter 2001) under revision - there will be increased emphasis on traceability of uncertainties in pH measurement. Here we describe how glass electrodes designed for measurement of pH are used in nuclear chemistry. The use of pH electrodes is then related to the IUPAC recommendations. In applied chemistry, e.g. nuclear chemistry, a pH is not sought as often as a hydrogen ion concentration or a simple equilibrium point during a titration. Ionic strengths are, moreover, often above the range in which the IUPAC recommendations apply. In these instances uncertainties must be assessed individually.     

Radical clock substrates, their C-H hydroxylation mechanism by cytochrome P450, and other reactivity patterns: what does theory reveal about the clocks' behavior?

There is an ongoing and tantalizing controversy regarding the mechanism of a key process in nature, C-H hydroxylation, by the enzyme cytochrome P450 (Auclaire, K.; Hu, Z.; Little, D. M.; Ortiz de Montellano, P. R.; Groves, J. T. J. Am. Chem. Soc. 2002, 124, 6020-6027. Newcomb, M.; Aebisher, D.; Shen, R.; Esala, R.; Chandrasena, P.; Hollenberg, P. F.; Coon, M. J. J. Am. Chem. Soc. 2003, 125, 6064-6065). To definitely resolve this controversy, theory must first address the actual systems that have been used by experiment, and that generated the controversy. This is done in the present paper, which constitutes the first extensive theoretical study of such two experimental systems, trans-2-phenylmethyl-cyclopropane (1) and trans-2-phenyl-iso-propylcyclopropane (4). The theoretical study of these substrates reveals that the only low energy pathway for C-H hydroxylation is the two-state rebound mechanism described originally for methane hydroxylation (Ogliaro, F.; Harris, N.; Cohen, S.; Filatov, M.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 8977-8989). The paper shows that the scenario of a two-state rebound mechanism accommodates much of the experimental data. The computational results provide a good match to experimental results concerning the very different extents of rearrangement for 1 (20-30%) vs 4 (virtually none), lead to product isotope effect for the reaction of 1, in the direction of the experimental result, and predict as well the observed metabolic switching from methyl to phenyl hydroxylation, which occurs upon deuteration of the methyl group. Furthermore, the study reveals that an intimate ion pair species involving an alkyl carbocation derived from 4 gives no rearranged products, again in accord with experiment. This coherent match between theory and experiment cannot be merely accidental; it comes close to being aproof that the actual mechanism of C-H hydroxylation involves the two-state reactivity revealed by theory. Analysis of the rearrangement modes of the carbocations derived from 1 and 4 excludes the participation of free carbocations during the hydroxylation of these substrates. Finally, the mechanistic significance of product isotope effect (different isotope effects for the rearranged and unrearranged alcohol products) is analyzed. It is shown to be a sensitive probe of two-state reactivity; the size of the intrinsic product isotope effect and its direction reveal the structural differences of the hydrogen abstraction transition states in the low-spin vs high-spin reaction manifolds.     

A Combined Theoretical and Experimental Approach to the Study of the Structural and Electronic Properties of Curcumin as a Function of the Solvent

Curcumin, a chemical compound present in the well-known Indian spice turmeric, has uses in many different fields ranging from medicinal chemistry to the dye industry. Its poor water solubility, though, makes Curcumin difficult to handle, making it less appealing for potential uses. The principal aim of this work is to perform a computational study of the structural and electronic properties of Curcumin {IUPAC name: 1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione} in several solvents, and a comparison with experimental data. Rotameric equilibria, vibrational and thermochemical analysis, and electronic absorption spectra (with ab initio and semi-empirical methodologies) have been studied, both in vacuum and in three selected solvents. Different computational techniques have been applied and the results compared. Combined approaches resulted in very satisfactory results. Interesting results have emerged, which suggest subsequent investigations about the nature of the excited states and potential derivatives of Curcumin that possibly have non-linear optical applications, as a π-core for innovative materials in laser engineering and photonics.     

Structure activity relationship by NMR and by computer: a comparative study

There has recently been considerable interest in using NMR spectroscopy to identify ligand binding sites of macromolecules. In particular, a modular approach has been put forward by Fesik et al. (Shuker, S. B.; Hajduk, P. J.; Meadows, R. P.; Fesik, S. W. Science 1996, 274, 1531-1534) in which small ligands that bind to a particular target are identified in a first round of screening and subsequently linked together to form ligands of higher affinity. Similar strategies have also been proposed for in silico drug design, where the binding sites of small chemical groups are identified, and complete ligands are subsequently assembled from different groups that have favorable interactions with the macromolecular target. In this paper, we compare experimental and computational results on a selected target (FKBP12). The binding sites of three small ligands ((2S)1-acetylprolinemethylester, 1-formylpiperidine, 1-piperidinecarboxamide) in FKBP12 were identified independently by NMR and by computational methods. The subsequent comparison of the experimental and computational data showed that the computational method identified and ranked favorably ligand positions that satisfy the experimental NOE constraints.     

Digital light-directed synthesis. A microarray platform that permits rapid reaction optimization on a combinatorial basis

Solution reactions using photogenerated reagents (Gao, X.; Yu, P.; LeProust, E.; Sonigo, L.; Pellois, J. P.; Zhang, H. J. Am. Chem. Soc. 1998, 120, 12698) are a potentially powerful means for combinatorial parallel synthesis of addressable molecular microarrays. In this report, we demonstrate that this chemistry permits combinatorial screening of reaction conditions on a microarray platform. Using this method of optimization and our reaction apparatus, efficient photogenerated acids and reaction conditions suitable for removal of the acid labile protection group on 5'-O of nucleotides are identified in a short period of time. The chemistry platform demonstrated opens new avenues for rapid, simultaneous investigation of multiple reactions using different reagents and reaction parameters directly on a solid support (e.g., a glass plate). The combinatorial screening method described may be extended to include general organic reactions employing photogenerated and conventional reagents as well as a microarray reaction device. This should be especially valuable for efficient synthesis of addressable organic compound libraries.     

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.     

将生物信息学与有机化学结合初探酶促反应原理与实践——介绍一个国外本科生实验并讨论其相关问题

21世纪是生命科学与信息科学高速发展的时代,化学作为理科的中心学科与此二者均有紧密的联系。伴随着各种交叉学科的诞生与发展,将信息科学技术整合有机化学方法并用于认知生物大分子进而解决生命科学问题也是大势所趋,而在生物化学与化学生物学基础教学中引入相关内容也具有前瞻性与必要性。国外化学本科的基础教育也切合时宜地以一个生物信息学的最常用软件PyMOL为例设计相关实验,让学生在了解反应中的有机化学机理的基础上,学习酶的三维结构,并探究酶催化该反应的原因。此设计结合了有机化学、生物化学、生物信息学、蛋白质结构生物学等多学科,可以加深学生对多肽与蛋白质的高级结构的认识,并为今后的生物化学学习与研究打下基础,同时有利于培养学生对于化学的兴趣,可谓一举多得。这对于培养交叉学科人才,做出开创性研究极为重要。对国内生物有机化学实验的设计有借鉴作用。     

Theoretical study of the electronic and optical properties of photochromic dithienylethene derivatives connected to small gold clusters

In the course of developing electronic devices on a molecular scale, dithienylethenes photochromic molecules constitute promising candidates for optoelectronic applications such as memories and switches. There is thus a great interest to understand and control the switching behavior of photochromic compounds deposited on metallic surfaces or nanoparticles. Within the framework of the density functional theory, we studied the effect of small gold clusters (Au3 and Au9) on the electronic structure and absorption spectrum of a model dithienylethene molecule. The molecular orbital interactions between the photochromic molecule and the gold cluster made it possible to rationalize some experimental findings (Dulic, D.; van der Molen, S. J.; Kudernac, T.; Jonkman, H. T.; de Jong, J. J. D.; Bowden, T. N.; van Esch, J.; Feringa, B. L.; van Wees, B. J. Phys. Rev. Lett. 2003, 91, 207402). For the closed-ring isomer, grafting a photochromic molecule on a small gold cluster does not change the characteristics of the electronic transition involved in the ring-opening reaction. On the opposite, the absorption spectrum of the photochromic open-ring isomer is strongly modified by the inclusion of the metallic cluster. In agreement with experimental results, our study thus showed that the cycloreversion reaction which involves the closed-ring isomer should be still possible, whereas the ring-closure reaction which involves the open-ring isomer should be inhibited. Connecting a dithienylethene molecule to a small gold cluster hence provides a qualitative comprehension of the photochromic activities of dithienylethenes connected to a gold surface.     

Advance of computational technology for simulating solvent extraction.

Due to recent significant enhancement of computer performance as well as computational techniques, molecular modeling and molecular simulations using computational chemistry can be achieved at the level of practical applications. Even in solvent extraction, the application of computational chemistry to simulations of extraction processes and the molecular design of high-performance extracting agents have gradually been increasing during the last decade. With combining the quantitative structure-property relationship between the molecule properties calculated by the computational chemistry methods and the thermodynamic properties obtained from experiments, researchers can precisely predict the next-generation of extracting agents and novel extraction processes. In this review, the concept of computational chemistry, such as molecular mechanics, molecular orbitals and molecular dynamics calculations, frequently used in the filed of solvent extraction, are outlined. Our systematic research on the solvent-extraction process utilizing MM, MO and MD calculations is also presented.     

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

New reaction simulator "LUMMOX" and its application for prediction of catalytic activities

We developed a new reaction simulator, "LUMMOX." It is an intermolecular interaction analyzer based on the theories of paired interacting orbitals (PIOs) and localized frontier orbitals (LFOs) that have been developed by Fujimoto et al. (Fukui, K.; Koga, N.; Fujimoto, H. J Am Chem Soc 1981, 103, 196; Fujimoto, H.; Koga, N.; Fukui, K. J Am Chem Soc 1981, 103, 7452; Fujimoto, H.; Satoh, S. J Phys Chem 1994, 98, 1436). LUMMOX runs on a Windows PC and displays graphic representation of orbital interactions. Prediction of activities, selectivities, and molecular weight of olefin polymerization catalysts are presented using PIO analysis and LFO calculation. Not only computational chemists but also experimental chemists can easily use this new system for catalyst design or molecular design from the point of view of orbital interaction.