By Shoji Takada
Department of Biophysics, Graduate School of Science, Kyoto University
Biomolecules are highly hierarchic and intrinsically flexible. Thus, computational modeling calls for multi-scale methodologies. We have been developing a coarse-grained biomolecular model where on-average 10-20 atoms are grouped into one coarse-grained (CG) particle. Interactions among CG particles are tuned based on atomistic interactions and by fitting physical properties with experiments. Here, we describe our CG modeling methodology for protein-DNA complexes, together with various biological applications, such as the DNA duplication initiation complex, model chromatins, and transcription factor dynamics on chromatin-like environment.
By Arun Yethiraj
University of Wisconsin
Macromolecular systems have interesting behavior on a range of length-scales and timescales. Computational study of these systems therefore requires modeling at multiple levels of detail. The development of coarse-grained (CG) models for macromolecules is an exciting and challenging frontier of research in computational chemistry. The ultimate goal is to develop a model that is computationally feasibly but captures the essential physical chemistry. I will discuss our recent efforts in this area. We have developed a CG model of water called the big multipole water (BMW) model which is in the spirit of the MARTINI model (four water molecules are grouped into one site) but includes electrostatic interactions including a quadrupole moment. I will discuss the performance of this force field for several problems including the hydrophobic effect, the behavior of peptides at membranes, the self-assembly and phase behavior of lipid/peptide mixtures, and the conformational properties of polymers. The results demonstrate the importance of electrostatic correlations in the water model, and suggest that these models can be useful in investigating complex fluids over long length-scales.
By Jiali Gao
Department of Chemistry, University of Minnesota
& Theoretical Chemistry Institute, Jilin University
An important question in enzymology is the precise mechanism by which large-scale motions and fast, local fluctuations are connected to the chemical transformation to lower the free energy barrier. In this talk, I will describe a combined QM/MM study of a hydrogen abstraction reaction, and compare the effects of distant mutation on the reaction rate and kinetic isotope effects with the wild-type enzyme. A novel multistate density functional theory is presented to describe a formally hydrogen atom abstraction involving coupled transfer of an electron and a proton.
By Yi Qin Gao
College of Chemistry and Molecular Engineering, Peking University
A simple theory of salt effects on water/air surface tension was formulated to take into account the interactions of individual ions with water. The theory predicts that the order of surface tension enhancement by salts is dependent on the solvation energy of cations and anions. The theory was then extended to understand how salts and other small molecules affect protein backbone solvation and protein secondary structure formation, with ion binding to the amide and ion pairing included. One of the most important predictions of the theory is that at low concentrations co-solutes rich in proton donors and those rich in proton acceptors have opposite effects and function as protein secondary structure denaturants and renaturants, respectively. For example, salts with strongly solvated hydrated cations and weakly solvated anions (e.g. MgI2 or even MgCl2) are expected to show strong salting-in effect, whereas salts with opposite cation versus anion properties, such as K2SO4, should have a strong salting-out effect. We also found that anion-cation cooperativity plays an important role in the understanding of the various experimental observations. MD simulations and thermodynamics calculations were then performed to understand ion-pairing in aqueous solutions, using a few simple salts as examples. In addition, it was found that the classical force fields with appropriately adjusted charge densities are capable of reproducing semi-quantatively the thermodynamic properties of electrolyte solutions.
- Lo Nostro, P.; Ninham, B. W. Hofmeister Phenomena: An Update on Ion Specificity in Biology. Chem. Rev. 2012, 112, 2286-2322.
- Zhang, Y. J.; Cremer, P. S. Chemistry of Hofmeister Anions and Osmolytes. Annu. Rev. Phys. Chem. 2010, 61, 63-83..4. Gao, Y. Q. Simple Theoretical Model for Ion Cooperativity in Aqueous Solutions of Simple Inorganic Salts and Its Effect on Water Surface Tension. J. Phys. Chem. B 2011, 115, 12466-12472.
- Gao, Y. Q. Simple Theory for Salt Effects on the Solubility of Amide. J. Phys. Chem. B 2012, 116, 9934-9943.
- Xie.w , Gao,Y.Q, A simple theory for Hofmeister Series, J. Phys. Chem. Lett. 2013,4,4247-4255.
By Qiang Cui
Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison
I’ll discuss challenges associated with understanding enzyme catalysis using hybrid QM/MM simulations, especially metalloenzymes that feature a dynamic active site and/or a high degree of solvent accessibility. Relevant examples include molecular motors, DNA repair enzymes and enzymes with a high degree of catalytic promiscuity. I’ll discuss recent developments in the density functional tight binding (DFTB) model and its integration with efficient sampling techniques (e.g., the thermal string approach) as well as with high-level QM/MM methods for more quantitative free energy computations. The developments are illustrated with several recent applications.
By Markus Meuwly
Correlating experimentally measurable quantities with the underlying atomic motions in condensed-phase systems is a challenging endeavor. Atomistic simulations have shown to provide such a link if accurate energy functions are employed and the processes of interest can be sampled for a sufficient amount of time. I will discuss application of such simulation techniques to modern spectroscopic techniques, such as 2-dimensional infrared spectroscopy, vibrational relaxation and chemical reactions treated with empirical force fields. The time scales inferred from experiment can then be interpreted at the structural level. The talk will highlight the prominent role of state-of-the art simulations in linking time-domain experiments with interpretations at the structural level.
- M. W. Lee, J. K. Carr, M. Goellner, P. Hamm and M. Meuwly J. Chem. Phys., 139, 054506 (2013)
- J. Huang, M. Buchowiecki, T. Nagy, J. Vanicek and M. Meuwly PCCP, 16, 204-211 (2014)
- J. Y. Reyes, T. Nagy and M. Meuwly PCCP, 16, 18533-18544 (2014)
- P. A. Cazade, F. Hedin, Z.-H. Xu and M. Meuwly J. Phys. Chem. B, 119, 3112-3122 (2015)
By Yundong Wu
Laboratory of Computational Chemistry and Drug Design, Peking University Shenzhen Graduate School, Shenzhen, 518055, China & College of Chemistry, Peking University, Beijing 100871, China
In this lecture, mechanistic studies of several catalytic C-H bond activation reactions will be discussed.1,2 (1) Mechanistic understanding has been developed for direct distal meta-C-H bond (more than ten bonds away) activation in tethered arene containing a remote nitrile. A dimeric Pd-Ag complex as active catalyst has been proposed.3 (2) A novel mechanism has been proposed to understand the effect of mono-protected amino acid as a ligand to promote the reactivity, regioselectivity,4 and stereoselectivity of Pd-catalyzed C-H bond activations.5 (3) The mechanism can be extended to understand the Pd-catalyzed viny-vinyl coupling reactions.6
- Cheng, G. J.; Zhang, X. H.; Chung, L. W.; Xu, L. P.; Wu. Y.-D. J. Am. Chem. Soc. 2015, 137, 1706.
- Chen, B.; Hou, X.-L.; Li, Y.-X.; Wu, Y.-D. J. Am. Chem. Soc. 2011, 133, 7668
- (a) Leow, D.; Li, G.; Mei, T.-S.; Yu, J.-Q. Nature 2012, 486, 518. (b) Yang, Y.-F. et. al. J. Am. Chem. Soc. 2014, 136, 344.
- Cheng, G.-J. et. al. J. Am. Chem. Soc. 2014, 136, 894.
- Cheng, G.-J. et. al. Chem. Eur. J. 2015, 21, 11180.
- Zhong X. M.; Cheng, G.-J.; Zhang, X. H.; Wu, Y.-D. Unpublished results.
By Zhipan Liu
Department of Chemistry, Fudan University
In this talk, I will introduce our recent development for the SSW package, including Stochastic Surface Walking method (SSW) and Double-Ended Surface Walking (DESW) method, and apply the package for resolving the reaction pathways in catalysis and solid phase transition. The SSW method is designed for the global optimization of structure on potential energy surface (PES), while maintaining the pathway information during structure search. By adding bias potentials and performing local relaxation repeatedly, SSW method can perturb smoothly the structure from one minimum to another following a random direction. The SSW method in combination with DESW method can be utilized for finding unknown structures and predicting chemical reactivity from molecules to solids. Using these methods, we recently studied a number of important systems, e.g. ZrO2 tetragonal-to-monoclinic phase transition, heterophase junction structures in photocatalysts, and dynamic catalyst structure evolution in H2 evolution.
- Guan, Shu-Hui；Zhang, Xiao-Jie; Liu, Zhi-Pan*, “Energy Landscape of Zirconia Phase Transitions”, J. Am. Chem. Soc., 2015, 137, 8010
- Zhao, Wei-Na; Zhu, Sheng-Cai; Li, Ye-Fei, Liu, Zhi-Pan* "Three-phase Junction for Modulating Electron-Hole Migration in Anatase/Rutile Photocatalysts", Chem. Sci., 2015, 6, 3483
- Wei, Guang-Feng; Liu, Zhi-Pan* "Restructuring and Hydrogen Evolution on Pt Nanoparticle", Chem. Sci., 2015, 6, 1485
- Zhang, Xiao-Jie; Liu, Zhi-Pan* "Reaction Sampling and Reactivity Prediction Using Stochastic Surface Walking Method", Phys. Chem. Chem. Phys., 2015, 17, 2757
- Shang, Cheng, Zhang, Xiao-Jie and Liu, Zhi-Pan*, “Stochastic Surface Walking Method for Crystal Structure and Phase Transition Pathway Prediction”, Phys. Chem. Phys. Chem. 2014, 16, 17845
- Zhang, Xiao-Jie; Shang, Cheng and Liu, Zhi-Pan*, “Double-Ended Surface Walking Method for Pathway Building and Transition State Location of Complex Reactions”, J. Chem. Theory Comput, 2013, 9, 5745;
- Shang, Cheng and Liu, Zhi-Pan*; “Stochastic Surface Walking Method for Structure Prediction and Pathway Searching”, J. Chem. Theory Comput, 2013, 9, 1838
By Zhigang Shuai
Department of Chemistry, Tsinghua University
Charge localization vs. electron coherence, nuclear tunneling effects vs. dynamic disorders and electron-phonon coupling, all these play essential roles in describing the charge transport in organic functional materials and consist of the major challenges for theoretical and computational chemistry. We found that (i) nuclear tunneling effect dominates; and (ii) dynamic disorder does not play appreciable roles; (iii) electron coherence is mostly dispensable for many systems but essential for bandlike transport. Electron-phonon couplings can be treated efficiently through a Wannier-interpolation algorithm applied to describe charge transport with the Boltzmann equation.
- Z. Shuai et al., Chem Soc Rev 2014, 43, 2662.
- Z. Shuai, et al. Acc. Chem. Res. 2014, 47, 3301.
By Todd Martinez
Novel computational architectures and methodologies are revolutionizing diverse areas ranging from video gaming to advertising and espionage. In this talk, I will discuss how these tools and ideas can be exploited in the context of theoretical and computational chemistry. I will discuss how insights gleaned from recommendation systems (such as those used by Netflix and Amazon) can lead to reduced scaling methods for electronic structure (solving the electronic Schrodinger equation to describe molecules), how the algorithms in electronic structure can be adapted for commodity stream processing architectures such as graphical processing units, and how nonlinear dimensionality reduction methods can be used to extract chemical knowledge from the resulting data. I will also show how these advances can be harnessed to progress from traditional “hypothesis-driven” methods for using electronic structure and first principles molecular dynamics to a “discovery-driven” mode where the computer is tasked with discovering chemical reaction networks. Finally, I will show how these can be combined with force-feedback (haptic) input devices and three-dimensional visualization to create molecular model kits which carry complete information about the underlying electrons. This interactive first principles molecular dynamics method (molecular computer-aided design) opens the door to novel ways of teaching chemistry and may also be of use in applied chemical research.
By Jun Li
Department of Chemistry, Tsinghua University, Beijing 100084, China
Nanocatalysis becomes a key frontier in heterogeneous catalysis due to rapid development of nano-sized materials. While small nanoparticles or subnanometer-sized clusters are often catalytically more active than their bulk materials, the stabilities of such particles or clusters tend to decrease. On the other hand, with the consumption of noble metals (e.g. Ru, Rh, Pd, Ag, Os, Ir, Pt, Au, etc.) as catalysts, how to reduce the usage of expensive noble metals also becomes a key concern in controlling the cost in catalytic industries. We have recently shown that singly dispersed atoms anchored on the surface of metal oxides demonstrate robust stability and significant catalytic activities. We coined such catalyst with singly dispersed atoms as single-atom catalyst (SAC), and suggested the notation M1/EOx for SACs with single-atom M1 supported on oxides EOx . Since then experimental and theoretical studies on SACs have become a hot topic in catalysis .
In this talk, we will provide an overview of the computational studies relevant to SACs using density functional theory (DFT) and wavefunction theory (WFT). The special stability and catalytic activity of selected SACs involving Ir1/FeOx, Pt1/FeOx, Au1/FeOx, Au1/CeO2-x, Rh1Co3/CoO1-x, Pt1@graphdiyne, and PdAu bimetallics will be explained on the basis of electronic structures and covalent chemical bonding [3-7]. Based on AIMD simulations we find that nano-catalysis can sometimes be achieved through dynamic single-atom catalysis (DSAC) . The catalytic mechanisms of SACs and DSAC will be discussed based on extensive DFT modeling and simulations.
- B.-T. Qiao, A.-Q. Wang, X.-F. Yang, L. F. Allard, Z. Jiang, Y.-T. Cui, J.-Y. Liu, J. Li, T. Zhang, "Single-Atom Catalysis of CO Oxidation Using Pt1/FeOx", Nature Chem., 2011, 3(8), 634−641.
- X.-F. Yang, A.-Q. Wang, B.-T. Qiao, J. Li, J.-Y. Liu, T. Zhang, "Single-Atom Catalysts: A New Frontier in Heterogeneous Catalysis", Acc. Chem. Res., 2013, 46(8), 1740-1748.
- J. Lin, A.-Q. Wang, B.-T. Qiao, X.-Y. Liu, X.-F. Yang, X.-D. Wang, J.-X. Liang, J. Li, J.-Y. Liu, T. Zhang, "Remarkable Performance of Ir1/FeOx Single-Atom Catalyst in Water Gas Shift Reaction", J. Am. Chem. Soc., 2013, 135(41), 15314-15317.
- J.-X. Liang , J. Lin , X.-F. Yang , A.-Q. Wang , B.-T Qiao , J.-Y. Liu , T. Zhang, J. Li, ”Theoretical and Experimental Investigations on Single-Atom Catalysis: Ir1/FeOx for CO Oxidation”, J. Phys. Chem. C, 2014, 118(38), 21945-21951.
- X. Wei, X.-F. Yang, A.-Q Wang, L. Li, X.-Y. Liu, T. Zhang, C.-Y. Mou, J. Li, "Bimetallic Au−Pd Alloy Catalysts for N2O Decomposition: Effects of Surface Structures on Catalytic Activity", J. Phys. Chem. C, 2012, 116(10), 6222−6232.
- B.-T. Qiao, J.-X. Liang, A.-Q. Wang, C.-Q. Xu, J. Li, T. Zhang, J.-Y. Liu, "Ultrastable Single-Atom Gold Catalysts with Strong Covalent Metal-Support Interaction (CMSI)", Nano Res., 2015, doi: 10.1007/s12274-015-0796-9
- S.-R. Zhang, L. Nguyen, J.-X. Liang, J.-J. Shan , J.-Y. Liu, A. I. Frenkel, A. Patlolla, W.-X. Huang, J. Li, F. Tao, "Catalysis on Singly Dispersed Bimetallic Sites", Nature Commun., 2015, 6, 7938.
- Y.-G. Wang, D.-H. Mei, V.-A. Glezakon, J. Li, R. Rousseau, "Dynamic Formation of Single-Atom Catalytic Active Sites on Ceria-Supported Gold Nanoparticles", Nature Commun., 2015, 6, 6511.
By Jinlong Yang
Hefei National Laboratory of Physical Science at the Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
Research on graphene and other two-dimensional (2D) materials, such as silicene, germanene, phosphorene, hexagonal boron nitride (h-BN), graphitic carbon nitride (g-C3N4), graphitic zinc oxide (g-ZnO) and molybdenum disulphide (MoS2), has recently received considerable interest owing to their outstanding properties and wide applications. Looking beyond this field, combining the electronic structures of 2D materials in ultrathin van der Waals heterojunctions has also emerged to widely study theoretically and experimentally to explore some new properties and potential applications beyond their single components. In this talk, I will review our recent theoretical studies on the structural, electronic, electrical and optical properties of 2D van der Waals heterojunctions using density functional theory calculations, including the Graphene/Silicene, Graphene/Phosphorene, Graphene/g-ZnO, Graphene/MoS2 and g-C3N4/MoS2 heterojunctions. Our theoretical simulations, designs and calculations show that novel 2D van der Waals heterojunctions provide a promising future for electronic, electrochemical, photovoltaic, photoresponsive and memory devices in the experiments.
By Keiji Morokuma
Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano-Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan
We have developed the Global Reaction Route Mapping (GRRM) strategy for automatic exploration of reaction pathways of complex molecular systems . The ADDF (anharmonic downward distortion following) and the AFIR (artificial force induced reaction) methods have been used for determination of not only energy minima and saddle points on the potential energy hypersurfaces but also minima and saddle points on the conical intersection and crossing seam hypersurfaces. I will discuss the methods and applications to several reaction systems, including photochemical reactions and organo and organometallic catalytic reactions.
- S. Maeda, K. Ohno and K, Morokuma, Systematic Exploration of the Mechanism of Chemical Reactions: Global Reaction Route Mapping (GRRM) Strategy by the ADDF and AFIR Methods, Phys. Chem. Chem. Phys., 15, 3683-3701 (2013);
- S. Maeda, T. Taketsugu, and K. Morokuma, Exploring Transition State Structures for Intramolecular Pathways by the Artificial Force Induced Reaction (AFIR) Method. J. Comp. Chem. 35, 166-173 (2014);
- S. Maeda, Y. Harabuchi, T. Taketsugu, and K.Morokuma, Systematic Exploration of Minimum Energy Conical Intersection Structures near the Franck-Condon Region, J. Phys. Chem. A 118, 12050-12058 (2014);
- S. Maeda, T. Taketsugu, K. Ohno and K. Morokuma, From Roaming Atoms to Hopping Surfaces: Mapping out Global Reaction Routes in Photochemistry. J. Am. Chem. Soc. 137, 3433–3445 (2015).