Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.

The Chemistry and Applications of Metal-Organic Frameworks

The chemistry of graphene oxide is discussed in this critical review Particular emphasis is directed toward the synthesis of graphene oxide, as well as its structure Graphene oxide as a substrate for a variety of chemical transformations, including its reduction to graphene-like materials, is also discussed This review will be of value to synthetic chemists interested in this emerging field of materials science, as well as those investigating applications of graphene who would find a more thorough treatment of the chemistry of graphene oxide useful in understanding the scope and limitations of current approaches which utilize this material (91 references)

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The chemistry of graphene oxide

The long-standing challenge of designing and constructing new crystalline solid-state materials from molecular building blocks is just beginning to be addressed with success. A conceptual approach that requires the use of secondary building units to direct the assembly of ordered frameworks epitomizes this process: we call this approach reticular synthesis. This chemistry has yielded materials designed to have predetermined structures, compositions and properties. In particular, highly porous frameworks held together by strong metal-oxygen-carbon bonds and with exceptionally large surface area and capacity for gas storage have been prepared and their pore metrics systematically varied and functionalized.

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Reticular synthesis and the design of new materials

ALTHOUGH CHEMISTS IN general are concerned with the art and science of constructing molecules and understanding their behavior, for a long time the idea that such molecules can be linked together by strong bonds to make infinite, extended structures was fraught with failure. The notion of using molecular building blocks to make such structures invariably led to chaotic, ill-defined materials and therefore not only defying the chemists’ need to exert their will on the design of matter but also preventing them from deciphering the atomic arrangement of such products. The field remained undeveloped for most of the twentieth century, and it was taken as an article of faith that linking molecules by strong bonds to make extended structures is a “waste of time” because “it doesn’t work.” This state of affairs was changed when a little known contribution was published 1994, where it was shown that negatively charged germanium sulfide clusters can be linked by positively charged manganese ions to make an extended structure (Figure 1).1 This was the first successful demonstration of linking molecular building blocks by strong bonds to make solid-state materials. The fact that the product was made in crystalline form and that the original clusters were translated into the crystal had two immediate ramifications: The crystallinity led to atomic level identification of the resulting structure while the preservation of the cluster geometry meant that in future the ability to predict accurately the outcome of such syntheses might become real especially since the cluster units are directional. There were additional advantages which became central to this emerging field. For example, the cluster constituents and their linkage (strong metal-sulfide bonds) provided the potential for making robust structures, and in the present case these Omar Yaghi Omar M. Yaghi obtained his Ph.D. from the University of Illinois-Urbana and was an NSF Postdoctoral Fellow at Harvard University. He currently holds the James and Neeltje Tretter Chair Professor of Chemistry at the University of California, Berkeley. He is the Founding Director of the Berkeley Global Science Institute and the Co-Director of the Kavli Energy NanoScience Institute. He is known for establishing reticular chemistry and developing new classes of porous, crystalline solids, termed metal-organic frameworks and covalent organic frameworks. He has been recognized by awards from fifteen countries, including the Wolf Prize in Chemistry (2018), U. S. National Academy of Sciences (2019), and the Royal Society of Chemistry Sustainable Water Award (2020). Although chemists in general are concerned with the art and science of constructing molecules and understanding their behavior, for a long time the idea that such molecules can be linked together by strong bonds to make infinite, extended structures was fraught with failure. The notion of using molecular building blocks to make such structures invariably led to chaotic, ill-defined materials and therefore not only defying the chemists’ need to exert their will on the design of matter but also preventing them from deciphering the atomic arrangement of such products. The field remained undeveloped for most of the twentieth century, and it was taken as an article of faith that linking molecules by strong bonds to make extended structures is a “waste of time” because “it doesn’t work.” by Cheng-Hsin Liu, Ha L. Nguyen, and Omar M. Yaghi https://doi.org/10.51167/acm00007 Cheng-Hsin Liu Cheng-Hsin Liu is pursuing a B.S. in Chemical and Biomolecular Engineering at the University of California, Berkeley. He is currently working with Professor Omar M. Yaghi on the structure modeling and characterization of reticular structures for carbon capture and other clean energy applications.

Reticular Chemistry and Harvesting Water from Desert Air

The mechanism of MOF crystal growth is fundamentally important to their design. In this issue of Chem, Deng and co-workers use an optical method to visualize and track the crystal interface during MOF growth. They derive a reaction kinetic equation for individual crystals of MOFs, thereby offering guidance to MOF synthesis. The mechanism of MOF crystal growth is fundamentally important to their design. In this issue of Chem, Deng and co-workers use an optical method to visualize and track the crystal interface during MOF growth. They derive a reaction kinetic equation for individual crystals of MOFs, thereby offering guidance to MOF synthesis. Reticulation of metal ions and charged organic units has led to ultraporous metal-organic framework (MOF) crystals.1Yaghi O.M. O’Keeffe M. Ockwig N.W. Chae H.K. Eddaoudi M. Kim J. Reticular synthesis and the design of new materials.Nature. 2003; 423: 705-714Crossref PubMed Scopus (8129) Google Scholar,2Férey G. Mellot-Draznieks C. Serre C. Millange F. Dutour J. Surblé S. Margiolaki I. A chromium terephthalate-based solid with unusually large pore volumes and surface area.Science. 2005; 309: 2040-2042Crossref PubMed Scopus (4244) Google Scholar The molecularly defined pores give rise to the utility of MOFs in a plethora of applications, such as CH4 storage,3Jiang J. Furukawa H. Zhang Y.-B. Yaghi O.M. High methane storage working capacity in metal−organic frameworks with acrylate links.J. Am. Chem. Soc. 2016; 138: 10244-10251Crossref PubMed Scopus (230) Google Scholar H2O capture from air,4Hanikel N. Pei X. Chheda S. Lyu H. Jeong W. Sauer J. Gagliardi L. Yaghi O.M. Evolution of water structures in metal-organic frameworks for improved atmospheric water harvesting.Science. 2021; 374: 454-459Crossref PubMed Scopus (138) Google Scholar and CO2 capture and conversion,5Choi K.M. Kim D. Rungtaweevoranit B. Trickett C.A. Barmanbek J.T.D. Alshammari A.S. Yang P. Yaghi O.M. Plasmon-enhanced photocatalytic CO2 conversion within metalorganic frameworks under visible light.J. Am. Chem. Soc. 2017; 139: 356-362Crossref PubMed Scopus (435) Google Scholar,6Jiang Z. Xu X.H. Ma Y.H. Cho H.S. Ding D. Wang C. Wu J. Oleynikov P. Jia M. Cheng J. et al.Filling metal-organic framework mesopores with TiO2 for CO2 photoreduction.Nature. 2020; 586: 549-554Crossref PubMed Scopus (339) Google Scholar making MOFs a new field in chemistry and materials science. Currently, the MOF family extends to more than 100,000 structures, some of which have already been produced at the ton scale. Although much progress in design and crystallization of MOFs is continually being made, understanding the mechanism for their formation remains less developed. The challenge is how to determine the impact of reaction conditions on the reticulation process and how to deconvolute each of these conditions to help understand their role in MOF crystal growth. Since the establishment of correlation between reaction rate and reactant concentration by Van’t Hoff, chemical kinetics studies played critical role in unraveling the mechanism of various chemical reactions. This classic tool is elegantly used in the study of MOF crystal growth as illustrated by Deng and co-workers in this issue of Chem.7Han J. He X. Liu J. Ming R. Lin M. Li H. Zhou X. Deng H. Determining factors in the growth of MOF single crystals unveiled by in situ interface imaging.Chem. 2022; 8: 1637-1657https://doi.org/10.1016/j.chempr.2022.03.006Abstract Full Text Full Text PDF Scopus (13) Google Scholar A flow cell was designed to offer precise control of temperature and concentration of the reactants, providing solid basis for systematically examining the crystal formation kinetics. In contrast to a sealed reaction system, the use of flow cell ensures the steady growth of MOF crystal and achieves a linear growth curve with nanometer accuracy. In this way, the reaction rate can be directly determined from the linear growth curve as the slope. The change of slope reflects the increase or decrease in the reaction rate when the temperature or the concentration of the reactant is varied systematically. An isolation method was applied, whereby only one variable is changed at a time. This allowed for the extraction of apparent reaction orders of metal ions and organic linkers separately. It is worth noting that an optical method is used in this work, in contrast to atomic force microscopy (AFM) or transmission electron microcopy (TEM) that would promise higher resolution.8Hosono N. Terashima A. Kusaka S. Matsuda R. Kitagawa S. Highly responsive nature of porous coordination polymer surfaces imaged by in situ atomic force microscopy.Nat. Chem. 2019; 11: 109-116Crossref PubMed Scopus (61) Google Scholar, 9Patterson J.P. Abellan P. Denny M.S. Park C. Browning N.D. Cohen S.M. Evans J.E. Gianneschi N.C. Observing the growth of metal-organic frameworks by in situ liquid cell transmission electron microscopy.J. Am. Chem. Soc. 2015; 137: 7322-7328Crossref PubMed Scopus (169) Google Scholar, 10Xing J. Schweighauser L. Okada S. Harano K. Nakamura E. Atomistic structures and dynamics of prenucleation clusters in MOF-2 and MOF-5 syntheses.Nat. Commun. 2019; 10: 3608Crossref PubMed Scopus (60) Google Scholar The special optic geometry of dark-field microscopy (DFM) beams the focus on the interface of the crystal rather than the bulk. This combined with the nondestructive nature of light and fast camera rate, 50 Hz, makes it ideally suited for the in situ tracking of interface during crystal growth in solution phase. A super-resolution/super-line technique is also developed to obtain the progression profile of interface with a trace resolution of 4 nm, sufficient to give an accurate reaction rate. The growth of individual crystals in the same camera view is monitored simultaneously, through which the reaction order of metal ion and organic linker, as well as activation energy, for each crystal are derived. Collective analysis of multiple crystals gave the data for several MOFs, each representing a different class of pores: Cu-MOF-74 (1D), Co-ZIF, Cu-MOF-2-BDC, Cu-MOF-2-NDC (2D), and HKUST-1 (3D). It is counterintuitive that, for all five MOFs, the reaction orders for metal ions and organic linkers are independent of the corresponding MOF chemical formulae; some are integers, but others are non-integers or negative. This means the conventional practice in MOF synthesis, where variations using the ratio of metal and linker in MOF structure, does not necessarily yield a suitable crystallization condition. The negative reaction order obtained for organic linker in the growth of HKUST-1 crystal is intriguing. It doesn’t mean that the addition of linkers inhibits crystal growth, but that excess linker will slow down the reaction, instead of accelerating it as commonly expected. The independence of the reaction rate from the chemical formula of MOF also indicates that the metal ions and organic linkers play different roles in the crystal growth process. With the experimental reaction orders in hand, the authors discussed the possible crystal growth mechanism as the most fascinating part of this work. A useful concept developed for the structure design of MOF is secondary building units (SBUs).1Yaghi O.M. O’Keeffe M. Ockwig N.W. Chae H.K. Eddaoudi M. Kim J. Reticular synthesis and the design of new materials.Nature. 2003; 423: 705-714Crossref PubMed Scopus (8129) Google Scholar The underlying geometry of the molecular building blocks and the directionality of their linkages in SBU dictate the overall topology of the resulting MOF. A recent study showed the presence of SBUs at the nucleation stage using TEM.10Xing J. Schweighauser L. Okada S. Harano K. Nakamura E. Atomistic structures and dynamics of prenucleation clusters in MOF-2 and MOF-5 syntheses.Nat. Commun. 2019; 10: 3608Crossref PubMed Scopus (60) Google Scholar However, a detailed picture of how the SBUs assemble at the crystal interface to grow into large single crystals remains unknown. The reaction orders measured by the current interface optical imaging work indicates that the formation of MOF crystal is unlikely to be an elementary reaction, but rather a multi-step process involving both the linkage and dissociation of the coordination bond between molecular building blocks. Taking 2D MOFs Cu-MOF-2-BDC and -NDC as examples, the possibilities of building block-by-building block addition and direct accumulation of Cu2L4 SBU (L represents the organic linker) on crystal interface are ruled out because neither of the derived reaction orders from the above scenarios matches with the experimental data. A new mechanism is proposed involving the formation of Cu2L4 SBU and its fragmentation into CuL2, giving a satisfactory match to the experimental reaction orders of both metal ion and organic linker (Figure 1). In this mechanism, the Cu2L4 SBU is a chemically more stable species, while the CuL2 growth unit is relatively more reactive and thus responsible for the MOF growth. The division of Cu2L4 is a critical step, providing fast equilibrium between these two species, hence generating sufficient CuL2 as the growth units for the following rate-determining step, where CuL2 combined with Cu2+ to join the active growth of MOF crystal interface (CuL)n. There surely are other possible mechanisms; this proposed new one offers the possibility that the SBU might be an important intermediate, but a different species might exist as the actual growth unit in the formation of MOF single crystal. Another interesting observation is the retreat and recovery of the crystal interface upon interruption, which can be associated with the accumulation and dissociation of the molecular building blocks. This further supports the multi-step nature of the crystal growth and points out the possible existence of a transition layer with structure and composition different from that of the crystal bulk (Figure 1). The stability of this reversible transition layer is also different from the crystal core, where the transition layer rather is dissolvable in the flow of pure solvent but not the crystal core. The thickness of the transition layer was measured and found to be dependent on the crystal size. It decreased as the crystal grew larger. The discovery of the transition layer shows not only that the temperature and reactant concentration are the determining factors for MOF crystal growth but also that the crystal interface itself is another critical one. This transition layer is reversible and stands as a bridge between the assembly of the molecular building blocks and the formation of crystalline bulk of MOF. The determining factors unveiled here fill in a missing piece in the crystal growth of MOFs. These studies not only help to elucidate the MOF crystal interface behavior at molecular level but are also likely to further guide the industrial production of MOFs. The nondestructive optical methods in combination with super-line technique developed in this study may very well prove suitable for the mechanistic examination of other important crystals in solution. The author declares no competing interests. Determining factors in the growth of MOF single crystals unveiled by in situ interface imagingHan et al.ChemMarch 28, 2022In BriefCrystal interface evolution is monitored by super-resolution technique during the growth of small MOF crystals into larger ones, in solution. The reaction orders for metal ion and organic linker are determined by isolation method and found to be independent from the corresponding MOF chemical formulas. This leads to the proposal of a new mechanism for MOF growth, involving the assembling and fragmentation of secondary building units, followed by fragment accumulation in a reversible transition layer at the interface of the MOF crystal. Full-Text PDF 

Evolution of MOF single crystals

Conventional storage of large amounts of hydrogen in its molecular form is difficult and expensive because it requires employing either extremely high pressure gas or very low temperature liquid. Because of the importance of hydrogen as a fuel, the DOE has set system targets for hydrogen storage of gravimetric (5.5 wt%) and volumetric (40 g/L) densities to be achieved by 2015. From our continuous efforts on hydrogen storage, it is believed that metalation of highly porous solids with high-valence metals is promising and provides a rational direction to realize high volumetric hydrogen density near room temperature. This grant was focused on the study of high surface area covalent organic frameworks (COFs) with these specific objectives (1) to introduce potential metal binding sites through the COF synthesis and (2) to implement metalation experiments and evaluate their respective hydrogen adsorption properties. To maximize our efforts, simulation calculations were also performed (prior to experiments) for the prediction of binding enthalpy of hydrogen for molecular building units containing transition metals and promising COF structures to increase volumetric hydrogen uptake at room temperature. In this effort, first molecular building units with optimal binding energy for hydrogen storage (20 kJ/mol) were designed by quantum mechanical (QM) methods. Employing more » these results, it was revealed that one of metalated COFs takes up 60 g/L (total) of H2 at 100 bar and 298 K. To realize proposed COF structures, chemistry of COF synthesis has been developed; for instance, new air stable COFs were synthesized via hydrazone (COF-41 to 43) and imine condensation (COF-301, 320, 340, and 366) and some of them were tested the effect on metalation. Finally, a new triazine COF with high volumetric hydrogen uptake capacity was presented as a proposed future direction. « less

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A Joint Theory and Experimental Project in the Synthesis and Testing of Porous COFs for On-Board Vehicular Hydrogen Storage

The phrase “selective oxidation” invokes the world of industrial chemistry concerned with the partial oxidation of organic molecules. There are two grounds for this. The first is economic, since almost half of the major products of the usage of heterogeneous catalysis (see Table I) are produced by selective oxidation of organic materials. The second ground for associating selective oxidation chemistry with the industrial community arises from the difficulty that academic chemists have encountered when attempting to understand heterogeneous selective oxidation processes on a molecular level and simulate them with homogeneous analogues. The detailed mechanisms of methanol dehydrogenation and ethylene epoxidation are unclear, and even the vaguest outlines of the C-H activation mechanism involved in xylene and butane oxidations are obscure.

Omar M. Yaghi

Papers

Reticular Chemistry and Harvesting Water from Desert Air

Evolution of MOF single crystals

A Joint Theory and Experimental Project in the Synthesis and Testing of Porous COFs for On-Board Vehicular Hydrogen Storage

Selective Oxidation Chemistry on Soluble Oxides: A Progress Report

Catenated covalent organic frameworks constructed from polyhedra