This question was answered in the: "chromedriver-users" google forum.
This is the working answer:
Map<String, Object> prefs = new HashMap<String, Object>();
prefs.put("profile.default_content_setting_values.notifications", 2);
ChromeOptions options = new ChromeOptions();
options.setExperimentalOption("prefs", prefs);
WebDriver driver = new ChromeDriver(options);
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