Statement_of_Work.docx

Chemical Structure Software Development Services

The National Institute of Standards and Technology (NIST) Mass Spectral Library group requires assistance for improvements in the 2-D chemical structures, and associated compound related information for enhancing the quality of its libraries.

I. SCOPE OF WORK

The contractor shall develop and deliver Microsoft Windows based user-interface software for computer-assisted improvement of chemical structures in the NIST Electron Ionization (EI) library.

II. SPECIFIC TASKS

a. The contractor shall design the product, in consultation with the Technical Point of Contact (TPOC), for use by NIST staff and contractors for quick, reliable examining and modifying of 2-D chemical structures in its libraries. This will involve both chemical structure ‘cleaning’ (equalizing bond lengths and angles to create chemical structures consistent with most structures already present in the library) and display of them symmetrically when possible. The contractor shall use International Union of Pure and Applied Chemistry (IUPAC) guidelines (https://www.iupac.org/publications/pac/pdf/2008/pdf/8002x0277.pdf) as well as, NIST prior practice for producing good quality structures.

b. As input, this program shall use chemical structures file in a standard text format (‘SDF’ – a standard for multiple structures in ‘MOL-file’ format), and output corrected chemical structures to another file in the same format. The input files will be provided by NIST.

c. The user interface shall show original and proposed corrected chemical structures, with the ability to ‘cut and paste’ structures. This will allow corrections by NIST evaluators, using available chemical structure drawing software (ACD ChemSketch or CambridgeSoft ChemDraw or custom software from the contractor).

d. Stereochemical improvements shall be proposed by the software, based on tables of information extracted from internet sources of structure/names/Chemical Abstracts Service Registry number and separate specific rules developed by the contractor.

e. ‘Cleaning’ structures may use publicly available chemical structure software or such processing can be developed for this program. This must be done automatically (without user intervention) by the software. If publicly available software is utilized, the contractor must include in their response a discussion of any life cycle costs such as software licensing fees that may be applicable.

f. The contractor shall extract from publicly available sources chemical names, chemical class and other information for use in enhancing NIST mass spectral libraries and for ordering new compounds for NIST measurement.

g. The contractor shall build a database of all available discrete, covalently bonded chemicals from all openly available internet sources that contain information that may be used to match compounds in NIST libraries (chemical structure, InChI, major identifiers, chemical formulas, etc.).

h. The contractor shall find all compounds of significance (defined as: listed in a major non-mass spectral compilation of compounds important for science or commerce such as the Toxic Substances Control Act inventory, Wikipedia) that are not present in either the NIST EI or Tandem libraries (library data provided by NIST). This shall include all available information concerning the origin and importance of the compound identities. This deliverable shall be submitted in an excel spreadsheet format. Specifically, the contractor shall extract chemical compound information from NIST libraries and process chemical compound information in chemical lists to generate a form compatible for NIST libraries/software. Processing implemented by the contractor shall de-salt compounds and reject mixtures or ambiguous compound identities.

i. For all compounds present in NIST libraries, the contractor shall provide all chemical information available from openly available internet sources, with developed quality control (QC) methods to limit incorrect entries. The description of the QC methods shall be provided to the TPOC. This shall include any possible imperfections in the NIST library as well as commonly used names not present in the library.

III. DELIVERABLES

YEAR I

TASK I - 6 Months: Deliver plans and a preliminary version of software capable of correcting chemical structures – using minimal level of stereochemical correction (up to two stereo centers).

TASK I - 12 Months: Deliver working 1.0 version of software

TASK II – 6 Months: Provide excel spreadsheet for at least six (6) major lists of chemicals of practical significance using as many web-based general lists as possible (PubChem, Chemspider, etc.

TASK II – 12 Months: Provide spreadsheet containing all compounds in the above lists that are not present in NIST libraries.

YEAR II

TASK I – 6 Months: Provide design and examples of software to add advanced stereochemical perception and to report relevant data available on the internet for each structure. Will also contain means of re-examining and correcting structures files processed by Version 1.0

TASK I – 12 Months: Provide Version 2.0 of software with advanced stereochemical perception and internet reporting.

TASK II – 6 Months: Add 12 more lists of chemicals on internet lists for data access and relevance for acquiring data.

TASK II – 12 Months: Provide updated list of chemicals to be ordered and information to be added to NIST libraries.

YEAR III

TASK I – 6 Months: Provide model of final version of structure correction software that may be used by customers of NIST libraries, which contain all available information for assisting correct stereochemical assignment.

TASK I – 12 Months: Deliver version 3.0 of software, capable of being used by customers of NIST libraries and external evaluators, along with full documentation of its use.

TASK II – 6 Months: Provide preliminary version designed to contain all available relevant data from internet sources that may be added to NIST libraries.

TASK II – 12 Months: Deliver final spreadsheet version containing all available information to be added to NIST libraries.

IV. KEY PERSONNEL QUALIFICATIONS

The contractor shall have at least one employee or subcontracted employee dedicated as Key Personnel. The Key Personnel shall have, at minimum, a Master’s degree in Chemistry, however a Doctorate degree is preferable. Also, the contractor shall possess at least 10 years of experience in computer programming for the processing of chemical structures, stereochemistry and names, and the extraction and organization of this information from available sources on the internet.

V. REPORTING

Reports of progress and proposed designs should be delivered no later than the 15th of the preceding month for each task. The contractor shall develop a work plan in collaboration with the NIST TPOC prior to development of any software or data delivery.

VI. PAYMENT TERMS

Advanced payments are not authorized. Partial payments are authorized. The Contractor may invoice monthly or quarterly in arrears after Government acceptance of deliverables.