Associate Principal Scientist, Small Molecule Chemical Engineering

Job Description

Associate Principal Scientist, Engineering

Chemical Commercialization Technology (CCT)

The Chemical Commercialization Technology (CCT) department, part of our Manufacturing Division, is seeking a highly motivated and collaborative scientist to join our team. This position offers the opportunity to provide technical leadership across a varied portfolio of late-stage small molecule development programs while working in a highly integrated environment with research, manufacturing, quality, regulatory and external partners.

The Associate Principal Scientist, Engineering, will leverage deep scientific and engineering knowledge to develop safe, robust, scalable, and commercially viable manufacturing processes. The role encompasses process characterization, technology transfer, process validation, regulatory filing support, commercial launch readiness and global supply support for late-stage pipeline and commercial products.

The successful candidate will lead teams in the application of scientific and risk-based approaches to process understanding and control strategy development. This includes the use of Quality Risk Management (QRM), statistical design of experiments (DOE), process modeling, and data analytics to enhance process robustness and ensure reliable product supply.

This position combines laboratory and pilot-scale experimental work with direct engagement at commercial manufacturing facilities. The scientist will be expected to provide strategic technical leadership during scale-up, process validation, technology transfer and manufacturing investigations while mentoring junior scientists and engineers.

The candidate must demonstrate a strong commitment to safety, quality, and compliance, including adherence to current Good Manufacturing Practices (cGMPs), Good Documentation Practices (GDPs), data integrity principles, and participation in risk assessments, deviation investigations, change control activities and continuous improvement initiatives.

Key Responsibilities

• Lead technical development, scale-up, and commercialization of small molecule drug substance manufacturing processes.

• Design and execute process characterization studies to establish process understanding and define commercial operating ranges.

• Apply Quality Risk Management (QRM), Quality by Design (QbD) and statistical methodologies to develop robust control strategies.

• Provide technical leadership for technology transfer activities to pilot plant and commercial manufacturing sites.

• Support process validation, continued process verification, regulatory submissions and post-approval change implementation.

• Collaborate effectively with Manufacturing, Process Research, Quality, Regulatory, Supply Chain and external partners to resolve complex technical issues.

• Lead investigations associated with process deviations, yield improvements, impurity control and process robustness.

• Mentor and develop junior scientists and engineers through technical coaching and project leadership.

• Drive innovation through the application of advanced process technologies, digital tools, modeling and data analytics where appropriate.

Position Qualifications

Education

• Ph.D. in Chemical Engineering or a related scientific discipline with a minimum of 4 years of relevant industrial experience following completion of the Ph.D.

OR

• B.S. or M.S. in Chemical Engineering or a related scientific discipline with a minimum of 8 years of relevant industrial experience.

Required Experience and Skills

• Demonstrated expertise in chemical process development and scale-up for pharmaceutical or specialty chemical manufacturing.

• Proven ability to independently design, execute, interpret, and communicate experimental studies aimed at improving process understanding, robustness, productivity and control strategy development.

• Experience supporting technology transfer from laboratory development through pilot plant and commercial manufacturing.

• Strong technical leadership and project management capabilities in cross-functional environments.

• Ability to mentor and develop scientists and engineers through technical guidance and coaching.

• Excellent written, verbal, and presentation communication skills.

• Strong organizational and time-management skills with the ability to manage multiple priorities.

• Demonstrated problem-solving capabilities using scientific and engineering principles.

• Ability to collaborate effectively across technical, quality, regulatory and manufacturing functions.

Preferred Experience and Skills

• Hands-on experience with unit operations commonly employed in small molecule drug substance API development and manufacturing, including chemical reactions, workup operations, filtration, drying, crystallization and particle engineering.

• Experience leading process characterization, validation strategy development, and process performance qualification (PPQ) activities.

• Experience authoring or contributing to regulatory submissions and responding to health authority questions.

• Expertise in statistical experimental design and data analysis tools (e.g., JMP, Minitab, or equivalent).

• Experience supporting commercial manufacturing, lifecycle management, and post-approval process changes.

• Familiarity with mathematical modeling, process simulation, mechanistic understanding and scale-up principles.

• Experience working with external manufacturing partners and contract development/manufacturing organizations (CDMOs).

• Knowledge of cGMP requirements and pharmaceutical manufacturing operations.

• Experience applying digital, data science, or advanced manufacturing technologies to accelerate process development and commercialization.

Required Skills:

API Manufacturing, Bioprocessing, Chemical Engineering, Chemical Processes, Commercialization, Manufacturing, Manufacturing Processes, Manufacturing Scale-Up, Manufacturing Technologies, Pharmaceutical Process Development, Process Design, Process Development (PD), Small Molecule Drugs, Technology Transfer

Preferred Skills:

Current Employees apply HERE

Current Contingent Workers apply HERE

US and Puerto Rico Residents Only:

Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please click here if you need an accommodation during the application or hiring process.

As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.  As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities.  For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:

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We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another’s thinking and approach problems collectively.

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The salary range for this role is

$142,400.00 - $224,100.00

This is the lowest to highest salary we in good faith believe we would pay for this role at the time of this posting. An employee’s position within the salary range will be based on several factors including, but not limited to relevant education, qualifications, certifications, experience, skills, geographic location, government requirements, and business or organizational needs.

The successful candidate will be eligible for annual bonus and long-term incentive, if applicable.

We offer a comprehensive package of benefits.  Available benefits include medical, dental, vision healthcare and other insurance benefits (for employee and family), retirement benefits, including 401(k), paid holidays, vacation, and compassionate and sick days. More information about benefits is available at https://jobs.merck.com/us/en/compensation-and-benefits.

You can apply for this role through https://jobs.merck.com/us/en (or via the Workday Jobs Hub if you are a current employee). The application deadline for this position is stated on this posting.

San Francisco Residents Only: We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance Ordinance

Los Angeles Residents Only: We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles’ Fair Chance Initiative for Hiring Ordinance

Search Firm Representatives Please Read Carefully 
Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company.  No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails. 

Employee Status:

Regular

Relocation:

Domestic

VISA Sponsorship:

Yes

Travel Requirements:

10%

Flexible Work Arrangements:

Not Applicable

Shift:

1st - Day

Valid Driving License:

No

Hazardous Material(s):

n/a

Job Posting End Date:

09/10/2026

*A job posting is effective until 11:59:59PM on the day BEFORE the listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.