Monolithiation of 5,5′‐Dibromo‐2,2′‐bithiophene Using Flow Microreactors: Mechanistic Implications and Synthetic Applications

The lithiation of 5,5′‐dibromo‐2,2′‐bithiophene with one equivalent of an alkyllithium such as n‐BuLi or s‐BuLi was studied by varying the residence time in flow microreactors. With a short residence time, the product 2,2′‐bithiophene (3) derived from dilithiation was obtained preferentially and a significant amount of the starting material 5,5′‐dibromo‐2,2′‐bithiophene remained unchanged. An increase in the residence time caused a higher yield of the product 5‐bromo‐2,2′‐bithiophene derived from monolithiation with expense in the yields of 2,2′‐bithiophene and 5,5′‐dibromo‐2,2′‐bithiophene. The lithiation using MeLi gave the product 5‐bromo‐2,2′‐bithiophene preferentially even with a very short residence time.     

Scalable and portable implementation of the fast multipole method on parallel computers

A scalable and portable Fortran code is developed to calculate Coulomb interaction potentials of charged particles on parallel computers, based on the fast multipole method. The code has a unique feature to calculate microscopic stress tensors due to the Coulomb interactions, which is useful in constant-pressure simulations and local stress analyses. The code is applicable to various boundary conditions, including periodic boundary conditions in two and three dimensions, corresponding to slab and bulk systems, respectively. Numerical accuracy of the code is tested through comparison of its results with those obtained by the Ewald summation method and by direct calculations. Scalability tests show the parallel efficiency of 0.98 for 512 million charged particles on 512 IBM SP3 processors. The timing results on IBM SP3 are also compared with those on IBM SP4.     

Practical Continuous‐Flow Controlled/Living Anionic Polymerization

A continuous‐flow reaction system was developed, allowing flow conditions of the entire system to be maintained at a predetermined constant level, which is one of the most significant factors for successful industrial application. Controlled/living anionic polymerization was selected as a model reaction since the characteristics of its polymer products, molecular weights, and molecular weight distributions are highly susceptible to changes in the relative flow rates of a monomer and initiator solutions. In flow microreactors, controlled/living anionic polymerization of styrene in tetrahydrofuran (THF)/hexane initiated by THF‐diluted n‐butyllithium (n‐BuLi) was examined. Poly(styrenes) of larger molecule sizes such as Mn > 15 000 were successfully synthesized. After continuous operation for four hours, ca. 0.5 kg of the polymer was readily produced with narrow molecular weight distribution, demonstrating the applicability of this continuous‐flow system for controlled/living anionic polymerization on considerably large scale with a view to its industrial usage in the future.     

Million atom molecular dynamics simulations of materials on parallel computers

Recent advances in computing tecnology — parallel computer architectures, portable software and development of robust O(N) algorithms — have revolutionized the field of computer simulation. Using the space-time multiresolution molecular dynamics algorithms it is possible to carry out multimillion atom simulations of materials in different ranges of density, temperature and uniaxial strain.     

Multiresolution atomistic simulations of dynamic fracture in nanostructured ceramics and glasses

Multimillion atom molecular-dynamics (MD) simulations are performed to investigate dynamic fracture in glasses and nanostructured ceramics. Using multiresolution algorithms, simulations are carried out for up to 70 ps on massively parallel computers. MD results in amorphous silica (a-SiO₂) reveal the formation of nanoscale cavities ahead of the crack tip. With an increase in applied strain, these cavities grow and coalesce and their coalescence with the advancing crack causes fracture in the system. Recent AFM studies of glasses confirm this behavior. The MD value for the critical stress intensity factor of a-SiO₂ is in good agreement with experiments. Molecular dynamics simulations are also performed for nanostructured silicon nitride (n-Si₃N₄). Structural correlations in n-Si₃N₄ reveal that interfacial regions between nanoparticles are amorphous. Under an external strain, nanoscale cavities nucleate and grow in interfacial regions while the crack meanders through these regions. The fracture toughness of n-Si₃N₄ is found to be six times larger than that of crystalline -Si₃N₄. We also investigate the morphology of fracture surfaces. MD results reveal that fracture surfaces of n-Si₃N₄ are characterized by roughness exponents 0.58 below and 0.84 above a certain crossover length, which is of the order of the size of Si₃N₄ nanoparticles. Experiments on a variety of materials reveal this behavior. The final set of simulations deals with the interaction of water with a crack in strained silicon. These simulations couple MD with a quantum-mechanical (QM) method based on the density functional theory (DFT) so that chemical processes are included. For stress intensity factor K=0.4 MPa m^1/2, we find that a decomposed water molecule becomes attached to dangling bonds at the crack or forms a Si-O-Si structure. At K=0.5 MPa m^1/2, water molecules decompose to oxidize Si or break Si-Si bonds.     

A divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactions

To enable large-scale atomistic simulations of material processes involving chemical reactions, we have designed linear-scaling molecular dynamics (MD) algorithms based on an embedded divide-and-conquer (EDC) framework: first principles-based fast reactive force-field (F-ReaxFF) MD; and quantum-mechanical MD in the framework of the density functional theory (DFT) on adaptive multigrids. To map these O(N) algorithms onto parallel computers with deep memory hierarchies, we have developed a tunable hierarchical cellular-decomposition (THCD) framework, which achieves performance tunability through a hierarchy of parameterized cell data/computation structures and adaptive load balancing through wavelet-based computational-space decomposition. Benchmark tests on 1920 Itanium2 processors of the NASA Columbia supercomputer have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations—0.56 billion-atom F-ReaxFF MD and 1.4 million-atom (0.12 trillion grid points) EDC–DFT MD—in addition to 18.9 billion-atom non reactive space–time multiresolution MD. The EDC and THCD frameworks expose maximal data localities, and consequently the isogranular parallel efficiency on 1920 processors is as high as 0.953. Chemically reactive MD simulations have been applied to shock-initiated detonation of energetic materials and stress-induced bond breaking in ceramics in corrosive environments.     

Scalable and portable visualization of large atomistic datasets

A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms.

Program summary

Title of program: AtomsviewerCatalogue identifier: ADUMProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUMProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics cardOperating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5Programming languages used: C++, C and OpenGLMemory required to execute with typical data: 1 gigabyte of RAMHigh speed storage required: 60 gigabytesNo. of lines in the distributed program including test data, etc.: 550 241No. of bytes in the distributed program including test data, etc.: 6 258 245Number of bits in a word: ArbitraryNumber of processors used: 1Has the code been vectorized or parallelized: NoDistribution format: tar gzip fileNature of physical problem: Scientific visualization of atomic systemsMethod of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data minimization, and levels-of-detail for minimal renderingRestrictions on the complexity of the problem: NoneTypical running time: The program is interactive in its executionUnusual features of the program: NoneReferences: The conceptual foundation and subsequent implementation of the algorithms are found in [A. Sharma, A. Nakano, R.K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X.L. Liu, T.J. Campbell, A. Haas, Presence—Teleoperators and Virtual Environments 12 (1) (2003)].     

Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids

A hybrid quantum mechanical/molecular dynamics simulation scheme is developed, in which a quantum mechanical system described by the density functional theory on real-space multigrids is embedded in a classical system of atoms interacting via an empirical interatomic potential. Handshake atoms coupling the quantum and the classical systems are treated by a novel scaled position method. The scheme is implemented on parallel computers using both task and spatial decompositions. An application to oxidation of Si (100) surface demonstrates seamless coupling of the quantum and the classical systems.