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Fluid mixtures are essential in an extremely wide range of practical applications and industrial processes. For example, heat pumps, air conditioners, refrigeration, chemicals (including fuels) production, purification, and separation, and environmental cleanup typically involve multiple coexisting fluids of differing composition (called phases). The amounts of each phase and their compositions change as conditions of temperature and/or pressure are varied - these changes also typically involve energy deposition or release by the fluid system. Accurate knowledge of this complex behavior is required for design, optimization, and control of these industrial devices and processes. Because laboratory determination of these many mixture properties is very expensive and time-consuming, it is highly desirable to have a computational means to determine this information. NIST’s new computer simulation methodology is capable of precisely and accurately predicting properties of fluid mixtures in record time. While molecular simulation is ideally suited for this, only within the last twenty years have methodological advances made this goal a realistic one. However, at the present state-of-the-art, simulation methods can calculate phase coexistence properties but only yield a single equilibrium point (a specific composition, temperature, pressure condition) per simulation. Therefore, a very large number of these simulations must be performed to obtain data over a range of thermodynamic conditions. This can require many days even for simple monatomic fluids. With NIST’s innovation, results are far more accurate and are realized in less than a single day! To validate this new approach, termed the mixture transition-matrix Monte Carlo method (M-TMMC), CSTL scientists investigated a number of model binary mixtures whose phase behavior is well known experimentally, and also mixtures that are known to pose problems for conventional computational approaches. This new method is beginning to be recognized by the chemicals industry as major breakthrough. In addition, it has attracted the attention of biologists for modeling the onset of multiple coexisting phases of large biomolecules such as proteins in solution.
“Determination of fluid-phase behavior using transition-matrix Monte Carlo: Binary Lennard-Jones mixtures”
Vincent K. Shen and Jeffrey R. Errington, J. Chem Phys. Vol 122, p. 064508 (2005).
Contact: Vincent K. Shen: e-mail: vincent.shen@nist.gov
After three years of development, a new, version of the NIST/EPA/NIH Mass Spectral Library has been released to the public. This evaluated reference collection, currently used alongside thousands of mass spectrometers, has been enlarged and extended to include additional classes of reference data:
Election Ionization Spectral Library: Approximately 20,000 EI spectra have been added to the library and the over all quality of the library has been improved by removing lower quality spectra and linking together spectra for compounds with closely related chemical structures. In addition, the naming and consistency of hundreds of compounds has been improved, including the application of new methods developed at NIST to identify and label different chemical structures. This enabled the co-evaluation of different, but closely related compounds expected to have similar spectra (stereoisomers and tautomers). With this edition, the library contains spectra for 163,000 compounds including over 27,000 replicate spectra for important compounds.
Gas Phase Retention Index (RI) Data and Estimates: This release also includes, for the first time, an evaluated collection of gas phase retention indices on non-polar columns. Correspondence of measured and reference retention indices along with mass spectra are generally considered to provide the ‘gold standard’ of identification of volatile organic compounds. This collection includes over 121,000 Kovacs retention indices for over 25,728 different compounds, over 12,000 of which have spectra in the NIST EI library. Most RI values were abstracted from the open literature, compared to each other and with estimates to find and remove errors. Using the information contained in this retention collection, a tool for estimating retention indices and their error limits for most compounds in the library has been added. This is expected to enable the removal of many false hits based on a spectral comparison alone.
MS/MS Spectra: This release also included a separate collection of over 2000 MS/MS spectra for diverse compounds. Most of these spectra have been measured on ion trap and triple quadrupole instrument using electrospray ionization, although spectra a number of other instrument types and ionization methods are represented. Instruments that generate such spectra have become standard tools in the analysis of biological and other complex samples, including the rapidly developing areas of proteomics and metabolomics. This is the first general purpose MS/MS library available to the public. Work is now underway to considerably expand the coverage of both chemical structures and instrument classes for the next release.
Contact: Steve Stein, e-mail: mailto:stephen.stein@nist.gov
Gary Mallard, e-mail: gary.mallard@nist.gov
Missile fuels pose operational requirements that are unlike those posed by other fuels. In a missile application, the liquid fuel is typically volume-limited rather than weight or mass limited, as an aircraft fuel would be. In missile operation, the primary operational consideration is fuel volumetric energy. In the mid 1970s, the highly successful fuel JP-10 was developed to meet this operational requirement. This fluid is essentially a single pure component: exo-tetrahydrodicyclopentadiene (tricyclo[5.2.1.0 2,6]decane, CAS No. 2825-82-3), for which accurate property information has been quite limited and not sufficient to support a recent U.S. Air Force effort to develop and assess new technologies for propulsion systems..
The Physical and Chemical Property Division was asked by the Fuels Branch of the Turbine Engine Division, AFRL, to provide this important property information. The work consisted of two parts: experimental measurements and modeling. The experimental aspects included the measurement of liquid density, viscosity, thermal conductivity, vapor pressure and velocity of sound behavior over the requisite ranges of temperature and pressure. Before these property measurements could be attempted, however, a comprehensive chemical analysis was done, and the fuel was tested for thermal decomposition. The property measurements were then performed so as to ensure the integrity of the fuel samples. The property data were then used, along with evaluated data from the literature, to develop numerical models that describes the properties of the fuel.
The model is based on a Helmholtz energy formulation, and has recently been provided to the Air Force along with a detailed report that describes the entire effort. This is the first such comprehensive report on this fuel, and will allow the Air Force and its contractors unprecedented possibilities for design optimization. A further reduction in the property uncertainties for this fluid, and extensions of the work to other fuels and potential fuels are being considered. Specific targets for fuel property and kinetics research, encompassing both standards and metrology issues, are being established in a series of workshops by the Air Force, industry, and academic researchers in cooperation with NIST staff.
Contact: Thomas J. Bruno, mailto:bruno@boulder.nist.gov
The NIST Chemistry WebBook (http://webbook.nist.gov/) is a site which distributes chemical and physical property data to users worldwide. An upgrade to the site in early June has provided translations for important parts of the site into four additional languages, Spanish, Portuguese, French, and Czech. The translations were developed by scientists in Europe with funding through the European Union’s project, “Eurospec – Access to Research Spectroscopic Data and Associated Chemical Knowledge – GTC1-2001-43000.” The translations were formatted and integrated into the site by personnel in the NIST Physical and Chemical Properties Division. English speakers will notice no change in the appearance of the site; speakers of the newly supported languages will automatically get the translated pages if their browser is configured to prefer one of the new languages over English.
As with prior releases, this release of the site contains numerous updates to its data collections, including two major changes that are of special interest. The first is a two fold increase in the number of molecules for which high accuracy physical property can be calculated based on equation of state data from NIST’s Boulder Laboratories. Physical property calculations can now be done for molecules as large as decane as well as a number of industrially important fluids (benzene, methanol and toluene) and all of the major refrigerants. The second major change is the addition of more than 126,000 gas chromatographic retention indices for over 27,000 compounds from the experimental literature. The retention index data is used in conjunction with mass spectrometry in analysis of a very wide range of applications from environmental samples, to chemical weapons, to drugs of abuse, to the detection of metabolic disorders in new-born infants.
In addition to the translated pages and updated data sets, the upgrade also added support for the IPUAC International Chemical Identifier. Developed by the International Union for Pure and Applied Chemistry (IUPAC) along with NIST, the identifier represents molecules in a form based on the connections between atoms in a molecule. As a new international standard, the identifier provides a tool to help chemists interchange data by providing reliable identification of molecular species.
Contact: Peter Linstrom e-mail: peter.linstrom@nist.gov
A new web site, http://www.hydrogen.gov/, has been created as a central point for all hydrogen- related information and activities within the federal government. As part of this effort, NI ST researchers in the Physical and Chemical Properties Division in Boulder have developed a web site (http://www.boulder.nist.gov/div838/Hydrogen/Index.htm) that is linked through the NI ST hydrogen web site (www.nist.gov/hydrogen) to the hydrogen.gov site. The new Division pages contain a wealth of information on the thermophysical properties of fluid hydrogen. The site includes a searchable bibliographic database on the properties of hydrogen compiled from the Cryogenic Data Center information center established at NI S T-Boulder in 1958, and also obtained from other resources such as databases of the TRC Group (Thermodynamics Research Center) of the Division. The literature references cover a time period from the late 1800’s to the present time. S everal very useful, but often hard-to-find NI S T publications on hydrogen are made available for download as PDF’s. As an example, NB S Monograph 168, S elected Properties of Hydrogen (Engineering Design Data), the 1981 publication by McCarty, Hord, and Roder is now readily available to potential users. In addition, we provide links to the NI S T Chemistry WebBook site (http://webbook.nist.gov/), also developed by researchers in the Physical and Chemical Properties Division. Here one may obtain properties of fluid hydrogen including PVT relationships, density, enthalpy, entropy, heat capacity, surface tension, Joule- Thomson coefficient, sound speed, viscosity, thermal conductivity, critical temperature, critical pressure, critical density, acentric factor, normal boiling point, vapor pressure (the saturation boundary) as well as additional chemical, thermochemical and physical properties of hydrogen including gas-phase thermochemistry data, phase-change data, reaction thermochemistry data, Henry’s Law data, gas-phase ion-energetics data, ion clustering data, mass spectrum, constants of diatomic molecules, and gas phase kinetics. The site provides a convenient central point for obtaining thermophysical properties information on fluid hydrogen.
Contact: Marcia Huber: e-mail marcia.huber@boulder.nist.gov
In order to address the significant demand for the application of theory and computational sciences in nanotechnology, the Physical and Chemical Properties Division in CSTL has created the NIST Center for Theoretical and Computational Nanosciences (NCTCN).
Most of the properties of materials at the nano-scale are governed by important quantum mechanical effects not observed in mesoscopic or macroscopic systems. The quantum mechanics governing the interactions between atoms and/or molecules in nanomaterials poses significant challenges to scientists fabricating or characterizing these materials, who for the most part are not able to predict the nature of such effects on their end-products or measurements. Nanoscience requires theoretical and computational methods that can complement and guide the experimental efforts leading to the creation of reliable techniques for characterization and metrology of physical and chemical properties of materials at the nanoscale.
The creation of a center of excellence in theoretical and computational nanosciences within NIST, enabling collaboration amongst the leaders in the field (both, at the national and international level), will be highly valuable in creating the necessary theoretical infrastructure that can complement and guide the rational design and characterization of novel nanoscale materials. In addition, this center will have a considerable impact in the efforts leading to improvements in the nanometrology, an area where NIST is expected to play a major role in the near future.
The activities of the Center will be mainly focused on:
1.- Develop, implement, and validate efficient and reliable theoretical methodologies and computational infrastructure required for understanding chemistry, physics, and biology at the nanoscale.
2.- Serve as a center for collaboration with scientists in industry, academia, and national labs to efficiently apply theory and simulation in the field of nanotechnology.
3.- Help industry identify and utilize effective computational solutions to problems limiting realization of the promise of nanotechnology.
The Center initially will involve the efforts of several NIST researchers from the Computational Chemistry Group in CSTL and collaborations with scientists across NIST. Also, seven guest researchers funded by the International Network of Emergent Science and Technology (INEST) created by Phillips Morris & Co., Ltd. (PMUSA) and the Altria Group, Inc will be joining the effort over the next few months. The overall activities of the Center will be coordinated by Dr. Carlos Gonzalez.
CONTACT: Carlos Gonzalez, e-mail: carlos.gonzalez@nist.gov
The September issue of the journal Fluid Phase Equilibria included an 85 page special section on the recently completed Second Fluid Properties Simulation Challenge. The champions of the Challenge, announced earlier at a meeting of the American Institute of Chemical Engineers, along with all of the participants in the Challenge, were invited to describe their efforts and focus on both the successes and barriers associated with the simulation of fluid systems. The industrial fluid properties challenge was established in 2001 to provide a realistic assessment of the value of molecular simulation methods for predicting thermophysical properties of industrially important fluids.
The description of bulk fluid properties based only on a knowledge of the molecular constituents remains one of the grand challenges associated with combining the successes of quantum chemistry, statistical mechanics, and computer technology. Yet practical applications of such an approach abound, and both an understanding of physical processes and quantitative predictions of property parameters are now feasible. Industry is keen to understand the capabilities and limitations of molecular simulation as a tool, and the Challenge has been designed to help in the assessment and drive improvements in the field.
The organizers of the Challenge, including researchers from major chemical companies and NIST Physical and Chemical Property Division partners, presented problems for which definitive answers were not yet known. A team, led by NIST researchers, was convened to perform and evaluate experimental measurements in order to provide the benchmark answers and uncertainties. The Champions of the challenge were those whose computer simulations were closest to physical systems: for predictions of phase information, Henry’s law constants, and heats of mixing of several systems. With the variety of questions posed and methods used, it is clear that in some cases simulation predictions would be useful in an industrial environment and for other situations, this technology is not yet adequate. An examination of the articles in this special section of Fluid Phase Equilibrium permits a unique perspective on both successes and failures of simulation approaches.
The organizing committee for the Challenge, consisting of scientists from NIST, Case Scientific, DuPont, Dow, Innovene, Exxon, Mitsubishi Chemical, and 3M, is working together to develop strategies to advance a vision for molecular simulation as an accepted tool for predicting thermophysical fluid properties for industry. A workshop for industrial, academic, and government experts is being planned, and additional information is available at http://fluidproperties.org/.
Contact: Anne Chaka e-mail: mailto:anne.chaka@nist.gov
Ray Mountain
e-mail: raymond.mountain@nist.gov
Daniel
Friend e-mail: mailto:raymond.mountain@nist.gov
Protein denaturation (i.e. the unfolding of a protein from its native conformation) generally leads to the formation of “denatured aggregates”. However, the cause and mechanism of this aggregation process are not well understood. More importantly, these aggregates pose significant health risks and challenges in both biological and pharmaceutical contexts. For example, the formation of denatured protein aggregates in vivo has been associated with a number of debilitating pathologies including Alzheimer’s, Parkinson’s, Huntington’s, and Creutzfeldt-Jakob’s diseases, as well as sickle cell anemia, Down’s syndrome, and cystic fibrosis. In the pharmaceutical industry, the aggregation of protein drugs during processing, storage, and delivery negatively impacts both their therapeutic value and their biological safety. As a result, there is an obvious and urgent need to understand the physical driving forces for protein denaturation and aggregation. Molecular simulation plays a crucial role in elucidating these poorly understood phenomena.
In spite of ever-increasing advances in computational power, conventional atomistic simulations of proteins in solution remain computationally demanding, and in many cases simply intractable, due to the sheer number of atoms involved and the macroscopic time scales often inherent in biological processes. Computational limitations have therefore necessitated the development of simplified, yet chemically and physically insightful, descriptions of intra- and inter-protein interactions and more efficient simulation approaches. To this end, a coarse-grained protein model was recently developed and demonstrated to correctly capture the effects of protein concentration, temperature, and elementary properties of protein sequence (composition) on the conformational stability of proteins in solution [1]; this basically provides a description of how native-state and denatured proteins interact in solution while accounting for their ability to fold and unfold. On the simulation front, recent advances in transition-matrix Monte Carlo algorithms have made it possible to calculate efficiently the free energy of multi-component systems [2-3], thereby yielding a complete description of the system’s thermodynamic properties including the formation of distinct solution phases; traditionally, this has proven to be a highly non-trivial task even for the simplest of systems. In a recent publication, CSTL researchers have collaborated to combine these two recent developments and investigate the interplay between native-state stability and the solution thermodynamics of globular proteins with different sequences [4].
One of the important findings of this work is that the formation of denatured aggregates appears to be driven by the thermodynamic tendency of the protein solution to phase separate or demix into two distinct liquids (similar to oil/water), one composed predominantly of folded proteins and the other of unfolded proteins. It is during the course of this demixing transition that the denatured aggregates form. Moreover, the model’s predicted trends for how protein sequence and environmental factors, such as temperature, affect the relative locations of the liquid-liquid demixing transition and the equilibrium unfolding curve on the phase diagram appear to be in good qualitative agreement with the experimentally observed solution behavior of hemoglobin and its sickle variant. While still at an early stage of development, the physical insights provided by this coarse-grained computational approach can potentially provide valuable guidance in the design, processing, and storage of protein therapeutics.
[1] J. K. Cheung and T. M. Truskett, Biophys. J.89,
1 (2005).
[2] V. K. Shen and J. R. Errington, J. Chem.
Phys.122, 064508 (2005).
[3] J. R. Errington and V. K.
Shen, J. Chem. Phys.123, 164103 (2005).
[4] V. K.
Shen, J. K. Cheung, J. R. Errington, and T. M. Truskett, submitted to
Biophys. J.
Contact: Vincent Shen e-mail: mailto:vincent.shen@nist.gov
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Last modified: 29 February 2000
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