Formation Enthalpies of C3 and C4 Brominated Hydrocarbons: Bringing Together Classical Thermodynamics, Modern Mass Spectrometry, and High-Level Ab Initio Calculations.

The enthalpies of formation of brominated C3-C4 hydrocarbons were critically evaluated using experimental data sources ranging from classical thermodynamics methods to modern high-precision mass spectrometry and reported in a time span of a century. The experimental data were used in conjunction with the results of modern high-level ab initio calculations. To facilitate quantitative analysis, a recently developed local coupled cluster-based computational protocol was extended to organic compounds containing univalent Br. Several erroneous data sources were identified in a course of the study. Possible reasons for the inconsistency between the ΔfHm° values recommended by the Committee on Data of the International Science Council (CODATA) and Active Thermochemical Tables for HBr in the gas and aqueous solution were discussed. The most up-to-date recommendations based on the comprehensive analysis of collected information are provided for 23 brominated hydrocarbons. For several compounds under consideration, the recommended values were previously lacking, while improved values and uncertainties were obtained for those with existing recommendations.

Towards improved FAIRness of the ThermoML Archive.

The ThermoML Archive is a subset of Thermodynamics Research Center (TRC) data holdings corresponding to cooperation between NIST TRC and five journals: Journal of Chemical Engineering and Data (ISSN: 1520-5134), The Journal of Chemical Thermodynamics (ISSN: 1096-3626), Fluid Phase Equilibria (ISSN: 0378-3812), Thermochimica Acta (ISSN: 0040-6031), and International Journal of Thermophysics (ISSN: 1572-9567). Data from initial cooperation (around 2003) through the 2019 calendar year are included. The archive has undergone a major update with the goal of improving the FAIRness and user experience of the data provided by the service. The web application provides comprehensive property browsing and searching capabilities; searching relies on a RESTful API provided by the Cordra software for managing digital objects. JSON files with a schema derived from ThermoML are provided as an additional serialization to lower the barrier to programmatic consumption of the information, for stakeholders who may have a preference of JSON over XML. The ThermoML and JSON files for all available entries can be downloaded from data.nist.gov (https://data.nist.gov/od/id/mds2-2422).

Efficient Ab Initio Estimation of Formation Enthalpies for Organic Compounds: Extension to Sulfur and Critical Evaluation of Experimental Data.

The efficient protocol for the estimation of gas-phase enthalpies of formation developed previously for C, H, O, N, and F elements was extended to sulfur. The protocol is based on a local coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] approximation and allows rapid evaluation of compounds with sizes computationally prohibitive to canonical CCSD(T) using quadruple zeta basis sets. As a part of model development, a comprehensive review and critical evaluation of experimental data were performed for 87 sulfur-containing organic and inorganic compounds. A compact model with only three empirical parameters for sulfur introduced to address the effects beyond frozen core CCSD(T) was developed. The model exhibits approximately 2 kJ·mol-1 standard deviation over a set of experimental values for a diverse collection of sulfur-containing compounds. The complete basis set version of the model demonstrates a similar performance and requires only one empirical parameter. Multiple problems with the existing experimental data were identified and discussed. In addition, a lack of reliable data for certain important classes of sulfur compounds was found to impede the model generalization and confident performance assessment.

Cys.sqlite: A Structured-Information Approach to the Comprehensive Analysis of Cysteine Disulfide Bonds in the Protein Databank.

Cysteine is a multifaceted amino acid that is central to the structure and function of many proteins. A disulfide bond formed between two cysteines restrains protein conformations through the strong covalent bond and torsions about the bond that prefer, energetically, ±90°. In this study, we transform over 30 000 Protein Databank files (PDBx/mmCIFs) into a single file, the SQLite database (Cys.sqlite). The database schema is designed to accommodate the structural information on both oxidized and reduced cysteines and to retain essential protein metadata to establish informational and biological provenance. Cys.sqlite contains over 95 000 peptide chains and 500 000 cysteines (700 000 structural conformers); there are over 265 000 cysteine disulfide bond conformations from structures solved with all available experimental methods. The structural information is analyzed with respect to sequence identity cutoff, the experimental method, and energetics of the disulfide. We find that as the experimental information becomes limiting and the influence of modeling becomes more pronounced, the observed average strain increases artificially. The database and analyses presented here can be used to improve the refinement of biological structures from experiments that are known to contain one or more disulfide bonds.

Critical evaluation of the enthalpies of formation for fluorinated compounds using experimental data and high-level ab initio calculations.

The ab initio method for prediction of the enthalpies of formation for CHON-containing organic compounds proposed earlier (J. Chem. Theory Comput. 2018, 14, 5920-5932) has been extended to their fluorinated derivatives. A single experimental Δf H o m is typically available for compounds in this scope. Thus, a priori evaluation of the data quality was found to be inefficient despite all available experimental data for C1─C3 hydrofluorocarbons and 34 data points for medium-size organofluorine compounds being considered. The training set was derived by analyzing consistency of the experimental and predicted values and removal of outliers. Significant issues in the experimental data, including inconsistency across different laboratories, were identified and potential causes for these problems were discussed. A conservative estimate of uncertainty for the experimental Δf H o m of organofluorine compounds was proposed.

Uncertainty quantification confirms unreliable extrapolation toward high pressures for united-atom Mie λ-6 force field.

Molecular simulation results at extreme temperatures and pressures can supplement experimental data when developing fundamental equations of state. Since most force fields are optimized to agree with vapor-liquid equilibria (VLE) properties, however, the reliability of the molecular simulation results depends on the validity/transferability of the force field at higher temperatures and pressures. As demonstrated in this study, although state-of-the-art united-atom Mie λ-6 potentials for normal and branched alkanes provide accurate estimates for VLE, they tend to over-predict pressures for dense supercritical fluids and compressed liquids. The physical explanation for this observation is that the repulsive barrier is too steep for the "optimal" united-atom Mie λ-6 potential parameterized with VLE properties. Bayesian inference confirms that no feasible combination of non-bonded parameters (ϵ, σ, and λ) is capable of simultaneously predicting saturated vapor pressures, saturated liquid densities, and pressures at high temperatures and densities. This conclusion has both practical and theoretical ramifications, as more realistic non-bonded potentials may be required for accurate extrapolation to high pressures of industrial interest.

Efficient DLPNO-CCSD(T)-Based Estimation of Formation Enthalpies for C-, H-, O-, and N-Containing Closed-Shell Compounds Validated Against Critically Evaluated Experimental Data.

An accurate and cost-efficient methodology for the estimation of the enthalpies of formation for closed-shell compounds composed of C, H, O, and N atoms is presented and validated against critically evaluated experimental data. The computational efficiency is achieved through the use of the resolution-of-identity (RI) and domain-based local pair-natural orbital coupled cluster (DLPNO-CCSD(T)) approximations, which results in a drastic reduction in both the computational cost and the number of necessary steps for a composite quantum chemical method. The expanded uncertainty for the proposed methodology evaluated using a data set of 45 thoroughly vetted experimental values for molecules containing up to 12 heavy atoms is about 3 kJ·mol-1, competitive with those of typical calorimetric measurements. For the compounds within the stated scope, the methodology is shown to be superior to a representative, more general, and widely used composite quantum chemical method, G4.

LOW-GWP REFRIGERANTS FOR MEDIUM AND HIGH-PRESSURE APPLICATIONS.

The merits of an alternative refrigerant are established based on many attributes including environmental acceptance, chemical stability in the refrigeration system, low toxicity, flammability, efficiency and volumetric capacity. In an earlier work, these criteria were used to screen a comprehensive database to search for refrigerants with low global warming potentials (GWP). The present paper summarizes the screening process and presents the performance of the 'best' replacement fluids for small and medium-sized air-conditioning, heating, and refrigeration applications. In addition to considering cycle calculations based only on thermodynamic properties, a simulation model that included transport properties and optimized heat exchangers was used to assess the performance potentials of the candidate fluids. The need for this more detailed modeling approach is demonstrated for systems relying on forced-convection evaporation and condensation. The study shows that the low-GWP refrigerant options are very limited, particularly for fluids with volumetric capacities similar to those of R 410A or R-404A. The identified fluids with good COP and low toxicity are at least mildly flammable. Refrigerant blends can be used to increase flexibility in choosing tradeoffs between COP, volumetric capacity, flammability, and GWP. The probability of finding 'ideal', better-performing low-GWP fluids is minimal.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 9. Extensible thermodynamic constraints for pure compounds and new model developments.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present article describes the background and implementation for new additions in latest release of TDE. Advances are in the areas of program architecture and quality improvement for automatic property evaluations, particularly for pure compounds. It is shown that selection of appropriate program architecture supports improvement of the quality of the on-demand property evaluations through application of a readily extensible collection of constraints. The basis and implementation for other enhancements to TDE are described briefly. Other enhancements include the following: (1) implementation of model-validity enforcement for specific equations that can provide unphysical results if unconstrained, (2) newly refined group-contribution parameters for estimation of enthalpies of formation for pure compounds containing carbon, hydrogen, and oxygen, (3) implementation of an enhanced group-contribution method (NIST-Modified UNIFAC) in TDE for improved estimation of phase-equilibrium properties for binary mixtures, (4) tools for mutual validation of ideal-gas properties derived through statistical calculations and those derived independently through combination of experimental thermodynamic results, (5) improvements in program reliability and function that stem directly from the recent redesign of the TRC-SOURCE Data Archival System for experimental property values, and (6) implementation of the Peng-Robinson equation of state for binary mixtures, which allows for critical evaluation of mixtures involving supercritical components. Planned future developments are summarized.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 8. Properties of material streams and solvent design.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present paper describes the first application of this concept to the evaluation of thermophysical properties for material streams involving any number of chemical components with assessment of uncertainties. The method involves construction of Redlich-Kister type equations for individual properties (excess volume, thermal conductivity, viscosity, surface tension, and excess enthalpy) and activity-coefficient models for phase equilibrium properties (vapor-liquid equilibrium). Multicomponent models are based on those for the pure-components and all binary subsystems evaluated on demand through the TDE software algorithms. Models are described in detail, and extensions to the class structure of the program are provided. Novel program features, such as ready identification of key measurements for subsystems that can reduce the combined uncertainty for a particular stream property, are described. In addition, new product-design features are described for selection of solvents for optimized crystal dissolution, separation of binary crystal mixtures, and solute extraction from a single-component solvent. Planned future developments are summarized.

ThermoData Engine (TDE) software implementation of the dynamic data evaluation concept. 7. Ternary mixtures.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported in this journal. The present paper describes the first application of this concept to the evaluation of thermophysical properties for ternary chemical systems. The method involves construction of Redlich-Kister type equations for individual properties (excess volume, thermal conductivity, viscosity, surface tension, and excess enthalpy) and activity coefficient models for phase equilibrium properties (vapor-liquid and liquid-liquid equilibrium). Constructed ternary models are based on those for the three pure component and three binary subsystems evaluated on demand through the TDE software algorithms. All models are described in detail, and extensions to the class structure of the program are provided. Reliable evaluation of properties for the binary subsystems is essential for successful property evaluations for ternary systems, and algorithms are described to aid appropriate parameter selection and fitting for the implemented activity coefficient models (NRTL, Wilson, Van Laar, Redlich-Kister, and UNIQUAC). Two activity coefficient models based on group contributions (original UNIFAC and NIST-KT-UNIFAC) are also implemented. Novel features of the user interface are shown, and directions for future enhancements are outlined.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 6. Dynamic web-based data dissemination through the NIST Web Thermo Tables.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe the development of a World Wide Web-based interface to TDE evaluations of pure compound properties, including critical properties, phase boundary equilibria (vapor pressures, sublimation pressures, and crystal-liquid boundary pressures), densities, energetic properties, and transport properties. This includes development of a system for caching evaluation results to maintain high availability and an advanced window-in-window interface that leverages modern Web-browser technologies. Challenges associated with bringing the principal advantages of the TDE technology to the Web are described, as are compromises to maintain general access and speed of interaction while remaining true to the tenets of dynamic data evaluation. Future extensions of the interface and associated Web-services are outlined.

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 5. Experiment planning and product design.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe development of an algorithmic approach to assist experiment planning through assessment of the existing body of knowledge, including availability of experimental thermophysical property data, variable ranges studied, associated uncertainties, state of prediction methods, and parameters for deployment of prediction methods and how these parameters can be obtained using targeted measurements, etc., and, indeed, how the intended measurement may address the underlying scientific or engineering problem under consideration. A second new feature described here is the application of the software capabilities for aid in the design of chemical products through identification of chemical systems possessing desired values of thermophysical properties within defined ranges of tolerance. The algorithms and their software implementation to achieve this are described. Finally, implementation of a new data validation and weighting system is described for vapor-liquid equilibrium (VLE) data, and directions for future enhancements are outlined.

ENTHALPY OF FORMATION OF AQUEOUS HYDROFLUORIC ACID: REVISION NEEDED?

Accurate enthalpies of formation of hydrofluoric acid in the gas and liquid states as well as in aqueous solutions are critical for reduction and interpretation of combustion calorimetry data for fluorinated compounds. Analysis of current recommendations reveals inconsistencies with the existing literature that can significantly affect experimental values derived using these recommendations. Through thorough and comprehensive analysis of available experimental data, including the sources not considered before, we provide recommendations that substantially improve consistency with these results. However, the scatter in the existing data also prevents further improvements and uncertainty reduction. New experimental data, particularly for aqueous HF solutions, are needed to advance.

ThermoData engine (TDE): software implementation of the dynamic data evaluation concept. 4. Chemical reactions.

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. This paper describes the first application of this concept to the evaluation of thermodynamic properties for chemical reactions. Reaction properties evaluated are the enthalpies, entropies, Gibbs energies, and thermodynamic equilibrium constants. Details of key considerations in the critical evaluation of enthalpies of formation and of standard entropies for organic compounds are discussed in relation to their application in the calculation of reaction properties. Extensions to the class structure of the program are described that allow close linkage between the derived reaction properties and the underlying pure-component properties. Derivation of pure-component enthalpies of formation and of standard entropies through the use of directly measured reaction properties (enthalpies of reaction and equilibrium constants) is described. Directions for future enhancements are outlined.

Web Thermo Tables - an On-Line Version of the TRC Thermodynamic Tables.

It has long been understood that availability of thermophysical and thermochemical property data is vital to scientific research and industrial design. For over 65 years, the Thermodynamics Research Center (TRC) has been publishing tables of critically evaluated data covering physical and thermodynamic properties of pure compounds, TRC Tables-Hydrocarbons and TRC Tables-Non-Hydrocarbons. Over their long history, the TRC Tables have always been valued as a reputable source of evaluated thermophysical and thermodynamic data. To facilitate more flexible, convenient, and up-to-date access to the data, here, we present the release of the on-line version of the TRC tables, Web Thermo Tables (WTT). Presently, WTT contains data for 7838 compounds and over 950,000 evaluated data points. The tabulated information includes critical properties, vapor pressures and boiling temperatures, phase transition properties, volumetric properties, heat capacities and derived properties, transport properties, reaction state-change properties, as well as index of refraction, surface tension, and speed of sound. Various search options and data plotting capabilities are provided via the Web interface. WTT are distributed through the NIST Standard Reference Data Program [1].

Efficient Estimation of Formation Enthalpies for Closed-Shell Organic Compounds with Local Coupled-Cluster Methods.

Efficient estimation of the enthalpies of formation for closed-shell organic compounds via atom-equivalent-type computational schemes and with the use of different local coupled-cluster with single, double, and perturbative triple excitation (CCSD(T)) approximations was investigated. Detailed analysis of established sources of uncertainty, inclusive of contributions beyond frozen-core CCSD(T) and errors due to local CCSD(T) approximations and zero-point energy anharmonicity, suggests the lower limit of about 2 kJ·mol-1 for the expanded uncertainty of the proposed estimation framework. Among the tested computational schemes, the best-performing cases demonstrate expanded uncertainty of about 2.5 kJ·mol-1, based on the analysis against 44 critically evaluated experimental values. Computational efficiency, accuracy commensurable with that of a typical experiment, and absence of the need for auxiliary reactions and additional experimental data offer unprecedented advantages for practical use, such as prompt validation of existing measurements and estimation of missing values, as well as resolution of experimental conflicts. The utility of the proposed methodology was demonstrated using a representative sample of the most recent experimental measurements.

Limited options for low-global-warming-potential refrigerants.

Hydrofluorocarbons, currently used as refrigerants in air-conditioning systems, are potent greenhouse gases, and their contribution to climate change is projected to increase. Future use of the hydrofluorocarbons will be phased down and, thus replacement fluids must be found. Here we show that only a few pure fluids possess the combination of chemical, environmental, thermodynamic, and safety properties necessary for a refrigerant and that these fluids are at least slightly flammable. We search for replacements by applying screening criteria to a comprehensive chemical database. For the fluids passing the thermodynamic and environmental screens (critical temperature and global warming potential), we simulate performance in small air-conditioning systems, including optimization of the heat exchangers. We show that the efficiency-versus-capacity trade-off that exists in an ideal analysis disappears when a more realistic system is considered. The maximum efficiency occurs at a relatively high volumetric refrigeration capacity, but there are few fluids in this range.

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing.

We propose a water-immersed nucleobase-functionalized suspended graphene nanoribbon as an intrinsically selective device for nucleotide detection. The proposed sensing method combines Watson-Crick selective base pairing with graphene's capacity for converting anisotropic lattice strain to changes in an electrical current at the nanoscale. Using detailed atomistic molecular dynamics (MD) simulations, we study sensor operation at ambient conditions. We combine simulated data with theoretical arguments to estimate the levels of measurable electrical signal variation in response to strains and determine that the proposed sensing mechanism shows significant promise for realistic DNA sensing devices without the need for advanced data processing, or highly restrictive operational conditions.

Isolation and characterization of high affinity aptamers against DNA polymerase iota.

Human DNA-polymerase iota (Pol ι) is an extremely error-prone enzyme and the fidelity depends on the sequence context of the template. Using the in vitro systematic evolution of ligands by exponential enrichment (SELEX) procedure, we obtained an oligoribonucleotide with a high affinity to human Pol ι, named aptamer IKL5. We determined its dissociation constant with homogenous preparation of Pol ι and predicted its putative secondary structure. The aptamer IKL5 specifically inhibits DNA-polymerase activity of the purified enzyme Pol ι, but did not inhibit the DNA-polymerase activities of human DNA polymerases beta and kappa. IKL5 suppressed the error-prone DNA-polymerase activity of Pol ι also in cellular extracts of the tumor cell line SKOV-3. The aptamer IKL5 is useful for studies of the biological role of Pol ι and as a potential drug to suppress the increase of the activity of this enzyme in malignant cells.