Although the winds of war were blowing across Europe in the late 1930's, Dutch universities were not generally affected until Clara was already into her graduate studies. The Germans occupied Holland in 1940, but initially left the universities alone. However, in 1941 the Germans dismissed all the Jewish professors at the universities throughout Holland. A young professor in Leiden spoke out against the dismissals and prompted a student strike that resulted in the Nazis immediately closing Leiden University until the war ended. Clara was allowed to take her exams and complete her Candidate's degree before she left.
The University at Utrecht was still open, so Clara continued her work there toward her Doctoral degree until the Germans required the signing of a loyalty oath by university students in 1943. From then on work at all universities (except at Leiden University which remained closed) continued on a much reduced scale. At that point Clara moved back home with her parents near Leiden while she commuted and worked for a professor at Delft.
During this time she was able to continue her studies at home and take small exams, when she felt she was ready, through personal contacts with professors in their homes. In this way she was qualified to take the final examination and receive her Doctoral degree in 1946 when the university opened again after the war. Her practical work had been completed in Utrecht and her course work during her years of studying at home.
Her major professor for the Ph.D. degree was Anton Eduard van Arkel, who had been her professor since she came to Leiden as an undergraduate.
A.E. van Arkel was a noted Dutch inorganic chemist who developed the theory of the chemical bond in inorganic chemistry based on the electrostatic interaction between ions. He was recently cited as the author of the "bond- type triangle," a diagram that represented the progressive transition between the three extreme cases of pure ionic, pure covalent, and pure metallic bonding. Clara had always found van Arkel very supportive of women in science and she recalls that he had a number of women on his staff. This no doubt contributed to the fact that 30% of the declared chemistry majors in 1938 at Leiden University were women.