The Mishnah continues with details, in regard to removing spiritual impurity through immersion in water, before praying or studying. Then, chapter four begins with laws in regard to the shemonah esrei. Prayers must be recited in a timely fashion, corresponding to the hours of the day, specifically, the position of the sun in the sky. This harkens back to Biblical passages concerning prayer in the Torah and the Book of Daniel (see Genesis 19:27, 24:63, 28:11; and, Daniel 6:10).
The prayer times generally correspond to the times that offerings were made during the day, based upon passages in the Torah. However, unlike morning and afternoon prayers, that are akin to the offerings, the evening prayer is not fixed to a specific time. Even though the ideal time is at twilight, when three stars appear in the sky, as mentioned previously in Berachos, the prayer can be said throughout the night.
Of course, G-d will listen to prayer of the heart at any time throughout the day and night. Rather, the above-mentioned prayer times have to do with the liturgical prayers found within the pages of the traditional Jewish siddur (prayerbook).