CARBONIZED FIBROUS RESIN AS A NEW SORBENT FOR SAMPLING POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) IN AMBIENT AIR

1. INTRODUCTION When investigating contaminated sites it is often essential to determine specific pollutants in a large number of ambient air samples. Amongst these sites, polycylic aromatic hydrocarbons (PAHs) are a major class of compounds that hav…     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

PRIRODA-04: a quantum-chemical program suite. New possibilities in the study of molecular systems with the application of parallel computing

Main characteristics are described of the PRIRODA quantum-chemical program suite designed for the study of complex molecular systems by the density functional theory, at the MP2, MP3, and MP4 levels of multiparticle perturbation theory, and by the coupled-cluster single and double excitations method (CCSD) with the application of parallel computing. A number of examples of calculations are presented.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 804–810, March, 2005.     

种植沙生植物--沙棘改善内蒙古地区生态环境

结合内蒙古地区现状，对沙棘的生物学和生态学特性、沙棘属植物化学成分和微量元素及种植沙生植物——沙棘的重要性和必要性进行了详细的研究和探讨。研究表明，沙棘属植物具有极强的生态适应性并富含多种营养成分和生物活性物质，并以耐干旱、耐瘠薄、萌蘖及固氮能力强等特点被称为治理非宜林地水土流失、改善生态环境的先锋树种。种植沙棘是治理内蒙古脆弱生态环境最经济、最有效的措施，是贫瘠的不毛之地发展经济、增加收入的经济树种。另外．种植沙棘的技术简便，容易掌握，投资少，见效快。     

Synthesis and Single Crystal Structure of a New Dinuclear Copper(II) Complex of 1,5-Bis(8-oxaquinoline)-3-methylpentane

A new flexible ligand, 1,5-bis(8-oxaquinoline)-3-methylpentane (C5MeOQ), was synthesized and used in the preparation of the new dinuclear copper(II) complex 1: [Cu₂(μ-OMe)₂(μ-C5MeOQ)(NO₃)₂]. Single crystal X-ray analysis revealed that complex 1 contains dinuclear Cu(II) units with bridging methoxo groups. The ligand, C5MeOQ, takes on a bent conformation in order to connect to and complete the square planar coordination environment of both copper centers; and one of the two Cu(II) centers adopts a distorted square planar configuration as a result of the ligand conformation. The magnetic properties of complex 1 were investigated by variable-temperature magnetic susceptibility measurements in the 100–300 K range. Interestingly, the susceptibility data for complex 1 reveals that the compound is diamagnetic, suggesting the presence of very strong antiferromagnetic coupling interactions between the adjacent Cu(II) centers.     

A parallel implementation of the COLUMBUS multireference configuration interaction program

Summary In this work a parallel implementation of the COLUMBUS MRSDCI program system is presented. A coarse grain parallelization approach using message passing via the portable toolkit TCGMSG is used. The program is very well portable and runs on shared memory machines like the Cray Y-MP, Alliant FX/2800 or Convex C2 and on distributed memory machines like the iPSC/860. Further implementations on a network of workstations and on the Intel Touchstone Delta are in progress. Overall, results are quite satisfactory considering the complexity and the prodigious requirements, especially the I/O bandwidth, of MRCI programs in general. For our largest test case we obtain a speedup of a factor of 7.2 on an eight processor Cray Y-MP for that section of the program (hamiltonian matrix times trial vector product) which has been parallelized. The speedup for one complete diagonalization iteration amounts to 5.9. An absolute speed close to 1 GFLOPS is found. Results for the iPSC/860 show that ordinary disk I/O is certainly not sufficient in order to guarantee a satisfactory performance. As a solution for that problem, the implementation of a fully asynchronous distributed-memory model for certain data files is in preparation. On leave from: Bereich Informatik, Universität Leipzig, Augustusplatz 10/11, O-7010 Leipzig, Germany     

Using a process-centered approach to minimize the effort of compliance

 The complexity of different quality standards can, in principle, be covered by different approaches and strategies. In-depth process mapping of quality control (QC) work streams was used by the analytical laboratories of Lonza AG to show up the principle differences in being compliant to different quality systems. The results identified two main drivers for all necessary actions: process-related activities and infrastructure-related activities. In addition, a clear indication of the economic impact of these driving forces was gained, which led the laboratories to decide on a process-oriented approach. This approach has the advantage of being able to reflect the different demands of different quality assurance (QA) regulations within the same QC organizational structure. Following the process helps avoid unnecessary efforts in analytical work and represents a very economical approach, at the same time, providing high flexibility to react to different QA or customer demands. Received: 5 July 2002 Accepted: 12 November 2002 Acknowledgements The process-oriented approach resulted from many, very challenging discussions for which I would like to thank the staff of my organization (Analytics & QC), especially, the QA staff and the LIMS team. Presented at Analytica Conference, 23–26 April 2002, Munich, Germany Correspondence to B. Ciommer     

Benchmark studies of the BCRLM reactive scattering code: Implications for accurate quantum calculations

Summary The Bending Corrected Rotating Linear Model (BCRLM), developed by Hayes and Walker, is a simple approximation to the true multidimensional scattering problem for reactions of the type: A + BC AB + C. While the BCRLM method is simpler than methods designed to obtain accurate three-dimensional quantum scattering results, this turns out to be a major advantage in terms of our benchmarking studies. The computer code used to obtain BCRLM scattering results is written for the most part in standard FORTRAN and has been ported to several scalar, vector, and parallel architecture computers including the IBM 3090-600J, the Cray XMP and YMP, the Ardent Titan, IBM RISC System/6000, Convex C-1 and the MIPS 2000. Benchmark results will be reported for each of these machines with an emphasis on comparing the scalar, vector, and parallel performance for the standard code with minimum modifications. Detailed analysis of the mapping of the BCRLM approach onto both shared and distributed memory parallel architecture machines indicates the importance of introducing several key changes in the basic strategy and algorithms used to calculate scattering results. This analysis of the BCRLM approach provides some insights into optimal strategies for mapping three-dimensional quantum scattering methods, such as the Parker-Pack method, onto shared or distributed memory parallel computers.     

Numerical solution of minimax problems of optimal control,part 1

This paper contains general transformation techniques useful to convert minimax problems of optimal control into the Mayer-Bolza problem of the calculus of variations [Problem (P)]. We consider two types of minimax problems: minimax problems of Type (Q), in which the minimax function depends on the state and does not depend on the control; and minimax problems of Type (R), in which the minimax function depends on both the state and the control. Both Problem (Q) and Problem (R) can be reduced to Problem (P).For Problem (Q), we exploit the analogy with a bounded-state problem in combination with a transformation of the Jacobson type. This requires the proper augmentation of the state vectorx(t), the control vectoru(t), and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.For Problem (R), we exploit the analogy with a bounded-control problem in combination with a transformation of the Valentine type. This requires the proper augmentation of the control vectoru(t) and the parameter vector , as well as the proper augmentation of the constraining relations. As a result of the transformation, the unknown minimax value of the performance index becomes a component of the parameter vector being optimized.In a subsequent paper (Part 2), the transformation techniques presented here are employed in conjunction with the sequential gradient-restoration algorithm for solving optimal control problems on a digital computer; both the single-subarc approach and the multiple-subarc approach are discussed.This research was supported by the National Science Foundation, Grant No. ENG-79-18667, and by Wright-Patterson Air Force Base, Contract No. F33615-80-C3000. This paper is a condensation of the investigations reported in Refs. 1–7. The authors are indebted to E. M. Coker and E. M. Sims for analytical and computational assistance.