Abstract. We present a comparison of the observed behavior of the F-region ionosphere over Millstone Hill during the geomagnetically quiet and storm periods of 6±12 April 1990 with numerical model calculations from the IZMIRAN time-dependent mathematical model of the Earth's ionosphere and plasmasphere. The major enhancement to the IZMIRAN model developed in this study is the use of a new loss rate of O 4 S ions as a result of new high-temperature¯owing afterglow measurements of the rate coe cients u 1 and u 2 for the reactions of O 4 S with N 2 and O 2 . The deviations from the Boltzmann distribution for the ®rst ®ve vibrational levels of O 2 v were calculated, and the present study suggests that these deviations are not signi®cant. It was found that the di erence between the non-Boltzmann and Boltzmann distribution assumptions of O 2 v and the di erence between ion and neutral temperature can lead to an increase of up to about 3% or a decrease of up to about 4% of the calculated NmF2 as a result of a respective increase or a decrease in u 2 . The IZMIRAN model reproduces major features of the data. We found that the inclusion of vibrationally excited N 2 v b 0 and O 2 v b 0 in the calculations improves the agreement between the calculated NmF2 and the data on 6, 9, and 10 April. However, both the daytime and nighttime densities are reproduced by the IZMIRAN model without the vibrationally excited nitrogen and oxygen on 8 and 11 April better than the IZMIRAN model with N 2 v b 0 and O 2 v b 0 . This could be due to possible uncertainties in model neutral temperature and densities, EUV¯uxes, rate coe cients, and the¯ow of ionization between the ionosphere and plasmasphere, and possible horizontal divergence of the¯ux of ionization above the station. Our calculations show that the increase in the O N 2 rate factor due to N 2 v b 0 produces a 5± 36% decrease in the calculated daytime peak density. The increase in the O O 2 loss rate due to vibrationally excited O 2 produces 8±46% reductions in NmF2. The e ects of vibrationally excited O 2 and N 2 on x e and e are most pronounced during the daytime.