Dr. Charles Brenner, who reigned for nearly a half-century as the dean of American psychoanalysis, working to clarify, refine and fiercely defend its core principles, died Monday in Manhattan. He was 94.

His death followed an emergency medical procedure at NewYork-Presbyterian/Weill Cornell hospital to relieve internal bleeding, said his niece Mary Brown.

A neurologist by training, Brenner applied his efforts to psychoanalysis, a ruthless scientific intellect that helped clarify Freud’s canon for working therapists and students, and eventually led him to formulate a theory of motivation that has had a profound effect on analytic treatment.

His 1955 book, “An Elementary Textbook of Psychoanalysis,” became a standard reference in training programs and sold more than a million copies, becoming the best-selling text on psychoanalysis by someone other than its inventor.

His landmark 1964 text, with Dr. Jacob Arlow, “Psychoana- lytic Concepts and Structural Theory,” extended Freudian thinking to argue that patients should understand not only the mental barriers underlying their distress but also exactly which thoughts were being blocked — say, a self-sabotaging guilt about success or an urge to be punished for feeling pleasure.

In a break from strict orthodoxy, Brenner argued that Freud’s concepts of the ego, the id and the superego were just that — concepts — and that the engine of human motivation was more like a psychological calculator, continuously computing ratios of pleasure versus pain: the gratification that would come from a love affair, for instance, versus the risk of discovery and abiding ache of guilt.

In analytic therapy, patients could reach a compromise between incompatible wishes that resolved some of the distress and was useful, Brenner argued.