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A century and a half-long story of graphite oxide has added much to its diversity and multivariance but did not make it absolutely bright as a substance. It can be referred to as a polymer with a unique structure, which can reversibly be 2D–3D transformed under the effect of such a widely used solvent as water. Each graphite oxide (GO) layer can be considered as an irregular polymer, which contains domains with different chemical properties. The layers are cross-linked and sewed by GO functional groups and water molecules, the role of latter depending on their relative content. When the amount of water is substantially increased, they are no longer sewing units, but dividing agents that provide the possibility of GO layers to exist independently. This peculiar feature of graphite oxide, which, being actually a complex organic substance, can change its properties when absorbing or releasing water, makes it very interesting subject of investigation. However, its experimental study can only provide information about its gross composition and some averaged characteristics. Even structural details of local GO sheet domains remain unclear. We have carried out nonempirical simulations of model GO sheet fragments with the aim to clarify the nature and possible location of its functional groups and their interaction with each other and with water molecules, which, judging from the experimental data, can never be completely removed from specimens under any drying conditions. For this purpose, different combinations of functional groups were added to basic C54 graphene fragment so that systems of the following general composition were considered: C54Hq(OH)k(O)l(O')m(COOH)n(H2O)p, where the numbers of OH hydroxide, О epoxide, O' keto, and COOH carboxyl groups varied in the ranges of 0≤k≤8, 0≤l≤3, 0≤m≤3, and 0≤n≤5, respectively. The number (n) of solvating water molecules was up to 12. Simulations were carried out at the density functional level with a B3LYP hybrid functional and 6-31G(d,p) extended Gaussian basis set. Simulated infrared absorption spectra were compared to the experimental spectra recorded for the specimens synthesized according to modified Hummer's method. For a number of experimental bands in characteristic and high-frequency ranges, a more reliable assignment was proposed that shed light on the prevailing structure motives, the role of water, and the nature of GO specimen's acidity.