  We analyze in detail the description of type IIB theory on a Calabi-Yau
three-fold near a conifold singularity in terms of intersecting D-branes. In
particular we study the singularity structure of higher derivative $F$-terms of
the form $F_g W^{2g}$ where $W$ is the gravitational superfield. This
singularity is expected to be due to a one -loop contribution from a charged
soliton hypermultiplet becoming massless at the conifold point. In the
intersecting D-brane description this soliton is described by an open string
stretched between the two D-branes. After identifying the graviphoton vertex as
a closed string operator we show that $F_g$'s have the expected singularity
structure in the limit of vanishing soliton mass.
