The wave function of matter is usually written with the electronic contributions separated from the nuclear in the classic Born-Oppenheimer approximation. This approximation is valid in most cases based on the clear separation in time scales for electron and nuclear motions. For thermally sampled coordinates, the electrons adiabatically follow the nuclear motions. The coupling to the bath and irreversible structural dynamics are determined by the time sale of the nuclear fluctuations. This approximation breaks down at conical intersections in which the change in electron distribution dictates the time scales for the structural dynamics. For optically excited systems, as discussed above, changes in the electron distribution are well above kT and persist long enough to affect nuclear motions. With atomically resolved dynamics, we have the perfect probe to connect this correlation between electron and nuclear coordinates. Independent information on the quantum state or electronic degrees of freedom can be obtained by conventional time resolved spectroscopy. The problem has been that the optical signatures are often obscured by the classic problem in spectroscopy of inhomogeneous broadening. The Miller group has developed a fully general optical analogue of NMR in which Coherent Control pulse shaping protocols have been implemented in a newly discovered interferometer design that is passively stabilized against phase noise (path length variations) [Opt. Express 17 (2009) 9764, Acc. Chem. Res. 42 (2009) 1442]. This new concept has made is possible to execute the same kind of coherence transfers among states as done in NMR but rather than spins, the relative phases and coherences of electronic states can be manipulated. The energy range of the states manipulated is in the range of chemical bonds. In this case, the objective is not to determine structure as in NMR (structural information is obtained via electron structural probes) but to manipulate the phase of the electronic wave function and thereby control dynamics and chemistry. This approach gives specific information on the phase of the wave function. It has also been shown that it is possible to control quantum decoherence to a certain degree by controlling the state preparation. This approach has been used to study the photoisomerization of bacteriorhodopsin in which electronic state evolution through the conical intersection has been manipulated. By virtue of the ability to rephrase the coherence, it has also been possible to selectively tag a frequency/state and directly monitor the state evolution through a conical intersection even for systems as complicated as biological molecules. This work has led to fundamental new insight into the difference between closed and open quantum systems with respect to weak field coherent control and has important implications in understanding the role of the bath in controlling reaction dynamics.