Clara decided to come to work with David Shoemaker at MIT, a decision which may have been influenced by the fact that she had a niece (the daughter of one of her half-brothers) who lived in Boston. Huberta Deliana Brink was married to the physicist Nicolaas Bloembergen (1981 Nobel laureate in Physics) who was on the faculty at Harvard. They had been introduced to each other by Clara in Holland when they were students.
David Shoemaker was working on metal phases, a study he started at Caltech under Linus Pauling, and X-ray crystallography was an important tool for determining phase structures. He wrote a comprehensive textbook entitled Experiments in Physical Chemistry (with C.G. Garland, and later with third author J.W. Nibler) that went through a number of revisions over the course of about 30 years. After Clara's first year with Shoemaker at MIT, he renewed her contract for a second year and at the end of that time they were married. She was destined never again to return to Leiden to work with van Arkel.
Clara worked with Barbara Low at Harvard Medical School for about a year after she married David Shoemaker. Low had done her Part II thesis with Hodgkin in 1943 and had completed her D.Phil. thesis with Hodgkin in 1948. During Clara's time in Low's laboratory Clara gave birth to her only child, a son who was healthy although he was premature. Within a month Clara developed a blood clot in her intestines and was seriously ill. Despite this, Clara continued to work with Low from home writing up the work she had done the previous year.
During the two years that Clara stayed at home with her son, she worked on International Tables of Crystallography. She was strongly encouraged to return to work by her husband and apparently that was her own desire as well. They found satisfactory day-care for their son, and she returned to work part time without any seeming problems adjusting to the demands of work and managing a household. Both she and her husband enjoyed working with students and inviting them to share the hospitality of their home.