Bauer, Susan Wise. The Story of Science: From the Writings of Aristotle to the Big Band Theory. W.W. Norton & Company, 2015.
Cooper, William. Great Physicists: The Life and Times of Leading Physicists from Galileo to Hawking. Oxford University Press, 2004. (See especially Ch. 16 on Bohr and Ch. 21 on Rutherford.)
Gray, Theodore. The Elements: A Visual Exploration of Every Known Atom in the Universe. Black Dog & Leventhal Publishers, 2009. (Please note that while this is not a children’s book, it contains photographs of the elements in the Periodic Table and information suitable for more mature students.)
Green, Dan. Discover More: The Elements. Scholastic, 2012.
Gribbin, John. The Scientists: A History of Science Told Through the Lies of Its Greatest Inventors. Random House, 2004. (See Ch. 10, Atoms and Molecules.)
Hakim, Joy. The Story of Science: Einstein Adds a New Dimension. Smithsonian Books, 2007. (See especially Chapters 13-16).
__________. The Story of Science: Newton at the Center. Smithsonian Books, 2005. (See especially Chapters 19, 27-29).
Heilbron, J. L. Ernest Rutherford and the Explosion of Atoms. (Oxford Portraits in Science). Oxford University Press, 2003.
Jackson, Tom. The Basics of Atoms and Molecules. Rosen, 2014.
McLean, Adam. What is Atomic Theory? (Shaping Modern Science). Crabtree, 2011.
Mooney, Carla. Chemistry: Investigate the Matter That Makes Up Your World. Nomad Press, 2016. (Includes timeline of discoveries)
Pasachoff, Naomi. Ernest Rutherford: Father of Nuclear Science (Great Minds of Science). Enslow, 2005.
Silverstein, Alvin, Virginia B. Silverstein and Laura Silverstein Nunn. Matter. Twenty-First Century Books, 2009.
See also the Elements series from Marshall Cavendish Benchmark.