The molecular geometries of polyyne chains H(CC)nH with their deprotonated forms (anions) have been optimized using ab initio LCAO-SCF molecular orbital (MO) method and density functional theory at different basis set levels. The polyynes possess a series of alternating single and triple bonds. On the theoretical side the persistence of bond alternation and the effect of chain lengthening on the individual bond length in linear conjugated polyyne chains has been investigated. The common conclusion has been drawn that the bond alternation will persist and that bond length variation will be small. The triple bond length increases progressively toward the asymptotic limits as the value of n increases progressively. If the split-valence basis set was employed, the total charges obtained using the Mulliken population analysis yielded unrealistic values. Using natural bond orbital (NBO) analysis or Bader's analysis, the net charges of the individual atoms converge very rapidly to their asymptotic limits, and the central atoms have almost zero charges in contrast to the Mulliken population analysis results. The reliability of deprotonation energies of neutral polyynes and their monoanionic derivatives calculated from the differences in molecular energy of the parent chains and the corresponding anions E(H(CC)n−)–E(H(CC)nH) and E(−(CC)n−)–E(H(CC)n−) was tested for different basis sets. The increase of the number of CC bonds in the chain decreases these differences asymptotically. The studied compounds are the best available building blocks in bimetallic compounds with useful properties in molecular electronics and nonlinear optics. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 82: 73–85, 2001