The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Parallelization is an effective way to reduce the computational time needed for molecular dynamics simulations. We describe a new parallelization method, the distributed-diagonal force decomposition method, with which we extend and improve the existing force decomposition methods. Our new method requires less data communication during molecular dynamics simulations than replicated data and current force decomposition methods, increasing the parallel efficiency. It also dynamically load-balances the processors' computational load throughout the simulation. The method is readily implemented in existing molecular dynamics codes and it has been incorporated into the CHARMM program, allowing its immediate use in conjunction with the many molecular dynamics simulation techniques that are already present in the program. We also present the design of the Force Decomposition Machine, a cluster of personal computers and networks that is tailored to running molecular dynamics simulations using the distributed diagonal force decomposition method. The design is expandable and provides various degrees of fault resilience. This approach is easily adaptable to computers with Graphics Processing Units because it is independent of the processor type being used.     

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly?A, poly?G, poly?C, poly?U), double-stranded DNA polynucleotides (poly?dAdT-poly?dAdT, poly?dGdC-poly?dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly?dAdT-poly?dAdT, at variance to preferred binding of Im and Py to only major groove of poly?dGdC-poly?dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.     

Controlling nonclassical content of clathrate hydrates through the choice of molecular guests and temperature

Low-temperature, low-pressure studies of clathrate hydrates (CHs) have revealed that small ether and other proton-acceptor guests greatly enhance rates of clathrate hydrate nucleation and growth; rapid formation and transformations are enabled at temperatures as low as 110 K, and cool moist vapors containing small ether molecules convert to mixed-gas CHs on a subsecond time scale. More recently, FTIR spectroscopic studies of the tetrahydrofuran (THF)-HCN double clathrate hydrate revealed a sizable frequency shift accompanied by a four-fold intensification of the C-N stretch-mode absorption of the small cage HCN, behavior that is enhanced by cooling and which correlates precisely with similar significant changes of the ether C-O/C-C stretch modes. These temperature-dependent correlated changes in the infrared spectra have been attributed to equilibrated extensive hydrogen bonding of neighboring large- and small-cage guest molecules with water molecules of the intervening wall. An ether guest functions as a proton acceptor, particularly so when complemented by the action of a proton-donor (HCN)/electron-acceptor (SO(2)) small-cage guest. Because guest molecules of the classic clathrate hydrates do not participate in hydrogen bonds with the host water, this H-bonding of guests has been labeled "nonclassical". The present study has been enriched by comparing observed FTIR spectra with high-level molecular orbital computational results for guests and hydrogen-bonded guest-water dimers. Vibrational frequency shifts, from heterodimerization of ethers and water, correlate well with the corresponding observed classical to nonclassical shifts. The new spectroscopic data reveal that the nonclassical structures can contribute at observable levels to CH infrared spectra for a remarkable range of temperatures and choice of guest molecules. By the choice of guest molecules, it is now possible to select the abundance levels of nonclassical configurations, ranging from ～0 to 100%, for a given temperature. This ability is expected to hasten understanding of the role of guest-induced nonclassical structures in the acceleration or inhibition of the rates of CH formation and transformation.     

Tb(Ⅲ)与PNIPAM接枝核壳纳米微球相互作用的研究

利用透射电镜、X射线光电子能谱、动态激光光散射和荧光光谱技术对Tb(Ⅲ)与聚N-异丙基丙烯酰胺(PNIPAM)接枝核壳纳米微球PNIPAM-g-P(NIPAM-co-St)(PNNS)的相互作用进行了研究.结果表明:Tb(Ⅲ)和热敏性的核壳纳米微球PNNS有显著的相互作用.其一,Tb(Ⅲ)可与PNNS中酰胺基团上的氧原子配位形成微球配合物Tb(Ⅲ)-PNNS;其二,Tb(Ⅲ)-PNNS微球配合物兼具热敏性;其三,该配合物在545 nm处的荧光强度较Tb(Ⅲ)增大了233倍,Tb(Ⅲ)与PNNS分子间能量传递达到50%,当Tb(Ⅲ)质量分数为12%时荧光强度最大.     

Mechanochemistry: opportunities for new and cleaner synthesis

The aim of this critical review is to provide a broad but digestible overview of mechanochemical synthesis, i.e. reactions conducted by grinding solid reactants together with no or minimal solvent. Although mechanochemistry has historically been a sideline approach to synthesis it may soon move into the mainstream because it is increasingly apparent that it can be practical, and even advantageous, and because of the opportunities it provides for developing more sustainable methods. Concentrating on recent advances, this article covers industrial aspects, inorganic materials, organic synthesis, cocrystallisation, pharmaceutical aspects, metal complexes (including metal-organic frameworks), supramolecular aspects and characterization methods. The historical development, mechanistic aspects, limitations and opportunities are also discussed (314 references).     

Polymerization-induced color changes of polydiacetylene-containing liposomes and peptide amphiphile fibers

Polydiacetylenes have received much attention due to their intrinsic optical properties. Their inclination to change color in response to environmental factors has been extensively exploited in the sensing of analytes. In this study we functionalized diacetylene-containing peptide amphiphiles and phospholipids with α-bromo esters so that they could be used as initiators in atom transfer radical polymerization (ATRP) reactions. Subsequently, the supramolecular assemblies formed by these molecules upon their addition to water, namely peptide amphiphile fibers and liposomes, were stabilized by polymerizing the diacetylene moieties present in the molecules. As a result, highly colored, disassembly resistant, macro initiators were created. To investigate whether steric crowding on the surface of these assemblies could influence the color of the polydiacetylenes, we utilized the initiator functionality that had been introduced prior to assembly in ATRP. We found that the chromatic properties of the polydiacetylenes were directly related to the formation of polymer on the surface of peptide amphiphile fibers as well as liposomes. Furthermore, we were able to demonstrate that the progress of this color change could be monitored with UV-visible spectroscopy.     

Can theory quantitatively model stratospheric photolysis? Ab initio estimate of absolute absorption cross sections of ClOOCl

We have calculated the absorption spectrum of dichlorine peroxide (ClOOCl) in the spectral range 250-400 nm. We have employed five different approaches to quantitatively model the absorption cross section (empirical broadening scheme, linearized harmonic reflection principle and full reflection principle with ground state density calculated using harmonic approximation, classical molecular dynamics, and path-integral molecular dynamics). We have also tested various single and multireference methods. We found that (i) the excitation characteristics of ClOOCl are sensitive on molecular geometries and therefore the ground state density has to be properly sampled and that (ii) single-reference methods tend to overestimate the absorption cross section and lead to a blueshift in the absorption maximum. The absorption spectrum calculated at the CASPT2 level with complete active space-configuration interaction (CAS-SCF) transition dipole moment with the ground state sampled via path-integral molecular dynamics is in a good agreement with the experiment. We, however, did not reach full agreement in the atmospherically relevant low-energy tail of the spectrum. The general message is that quantitative predictions are difficult even for a relatively small molecule as ClOOCl and the convergence, with respect to the electronic structure method, basis set used, and ground state sampling, needs to be carefully examined.     

Hydrogen bond dynamics in the excited states: photodissociation of phenol in clusters

We have investigated the photodynamics of phenol molecules in clusters. Possible reaction pathways following the photoexcitation of hydrogen-bonded phenol clusters have been identified theoretically using ab initio calculations. Experimentally we have studied the phenol molecules and clusters of various size distributions in a molecular beam apparatus. In particular, we have measured the H-fragment kinetic energy distributions after the excitation with 243 nm and 193 nm laser radiation. At 243 nm the KED spectra did not show any significant difference between the photodissociation of isolated molecules and phenol in larger clusters, while at 193 nm the contribution of the fast H-fragments is significantly suppressed in clusters with respect to the bare phenol molecule. We have interpreted the experimental results within the framework of the suggested reaction pathways.     

Reactivity of lithium n-butyl amidinates towards group 14 metal(II) chlorides providing series of hetero- and homoleptic tetrylenes

The new class of homo- and heteroleptic n-butyl-N,N'-disubstituted amidinato group 14 metal(II) complexes were prepared by salt elimination from starting lithium amidinates and metal(II) chlorides both in stoichiometric ratio 2:1 and 1:1, respectively. The target amidinates contain less bulky isopropyl or cyclohexyl as well as a sterically demanding aromatic substituent. Desired 1:1 Pb(II) complexes are not accessible by the described procedure. Ligand transfer from Pb to Sn is taking place if homoleptic Pb(II) compounds are reacted with SnCl(2). Prepared tetrylenes were characterized by (1)H, (13)C, (119)Sn and (207)Pb NMR spectroscopy in C(6)D(6) or THF-d(8). X-Ray diffraction studies of one heteroleptic Ge(II) monomeric where the coordination polyhedron of the three coordinated germanium atoms is a trigonal pyramid, two different dimeric structures of heteroleptic Sn(II) complexes, one amidine hydroiodide byproduct and the oxidation product of the heteroleptic chloro Sn(II) amidinate as a tetranuclear species with two Sn(IV) and two Sn(II) atoms in central Sn(2)O(2) planar ring were performed on appropriate single crystals. The dimer of one of the heteroleptic stannylenes reveals a new type of monomeric units connection, weak Sn-Cl contact and an interaction of the tin atom with delocalized N-C(C)-N system of the amidinato ligand of the second molecule.     

Soft-templating synthesis of mesoporous magnetic CuFe2O4 thin films with ordered 3D honeycomb structure and partially inverted nanocrystalline spinel domains

Combining sol-gel chemistry with polymer templating strategies enables production of CuFe(2)O(4) thin films with both an ordered cubic network of 17 nm diameter pores and tunable spinel domain sizes. These nanocrystalline materials contain only minor structural defects with λ = 0.85 ± 0.02 and exhibit multiple functionalities, including superparamagnetic behavior (T(B)≈ 310 K) and redox- and photoactivity.