In order to examine covalence and polaron effects in the bilayer manganite ${\mathrm{La}}_{2\ensuremath{-}2x}{\mathrm{Sr}}_{1+2x}{\mathrm{Mn}}_{2}{\mathrm{O}}_{7}$, we have performed molecular orbital cluster calculations. Two types of ${({\mathrm{Mn}}_{2}{\mathrm{O}}_{11})}^{15\ensuremath{-}}$ clusters, one with the manganese aligned in the $a$ direction and the other in the $c$ direction, were embedded in a point charge environment that mimicked the crystal environment of the bilayer manganite at $x=0.40$, and their electronic states were calculated by the unrestricted Hartree-Fock (UHF) and the complete active-space self-consistent field (CASSCF) methods. The CASSCF result for the cluster along the $a$ direction exhibits double-well potential energy surfaces for symmetry-breaking deformations. This indicates small polaron formation in this system. On the other hand, the UHF calculation did not give double-well potential surfaces, showing the importance of the electron correlation for the polaron formation. Significantly large wells are obtained for the in-plane antiphase breathing and in-plane antiphase $\mathrm{O}\mathrm{Mn}\mathrm{O}$ stretching deformations. The double-well barrier for the former is $68\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$ and that for the latter is $92\phantom{\rule{0.3em}{0ex}}\mathrm{meV}$, where the former is close to the experimentally obtained polaron hopping activation energy above ${T}_{\mathrm{c}}$. A similar calculation for the cluster along the $c$ direction exhibits a negligibly small double well, indicating that the polaron effect is very small in the carrier hopping in the $c$ direction within a bilayer. Electronic structures have been investigated using natural orbitals. At a double-well minimum, a localized polaron orbital is seen. In the ground state, a small but significant hole population is found in $p$ orbitals of the bridging oxygen, and a slight electron population is found in the ${e}_{g}$ orbital above the localized polaron orbital. For the cluster along the $a$ direction and without deformation, the first excited state is an electron-transfer state where an electron is moved from the bridging oxygen ${p}_{z}$ to a manganese ${e}_{g}$ orbital. This excited state couples with the ground state by the pseudo-Jahn-Teller effect, thus, the polaron is the ``pseudo-Jahn-Teller polaron.'' Using the natural orbitals, we have calculated magnetic Compton profiles and compared with experiment. Comparison between the experimental and theoretical results suggests the presence of polarons below ${T}_{\mathrm{c}}$. We briefly discuss the implication of this result in relation to the colossal magnetoresistance effect.
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