We analyze in detail the description of type IIB theory on a Calabi-Ya
u three-fold near a conifold singularity in terms of intersecting D-br
anes. In particular, we study the singularity structure of higher deri
vative F-terms of the form FgW2g where W is the gravitational superfie
ld. This singularity is expected to be due to a one-loop contribution
from a charged soliton hypermultiplet becoming massless at the conifol
d point. In the intersecting D-brane description this soliton is descr
ibed by an open string stretched between the two D-branes. After ident
ifying the graviphoton vertex as a closed string operator we show that
F-g's have the expected singularity structure in the limit of vanishi
ng soliton mass.