A description of the ab initio quantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed-shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speedup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. 0 1993 by John Wiley & Sons, Inc.

DsRed, a brilliantly red fluorescent protein, was recently cloned from Discosoma coral by homology to the green fluorescent protein (GFP) from the jellyfish Aequorea. A core question in the biochemistry of DsRed is the mechanism by which the GFP-like 475-nm excitation and 500-nm emission maxima of immature DsRed are red-shifted to the 558-nm excitation and 583-nm emission maxima of mature DsRed. After digestion of mature DsRed with lysyl endopeptidase, high-resolution mass spectra of the purified chromophore-bearing peptide reveal that some of the molecules have lost 2 Da relative to the peptide analogously prepared from a mutant, K83R, that stays green. Tandem mass spectrometry indicates that the bond between the alpha-carbon and nitrogen of Gln-66 has been dehydrogenated in DsRed, extending the GFP chromophore by forming OCANOCAO at the 2-position of the imidazolidinone. This acylimine substituent quantitatively accounts for the red shift according to quantum mechanical calculations. Reversible hydration of the CAN bond in the acylimine would explain why denaturation shifts mature DsRed back to a GFP-like absorbance. The CAN bond hydrolyses upon boiling, explaining why DsRed shows two fragment bands on SDS͞PAGE. This assay suggests that conversion from green to red chromophores remains incomplete even after prolonged aging. In the preceding companion paper (1), we showed that the red fluorescent protein DsRed cloned from coral by Matz et al. (2) has impressive brightness and stability against pH changes, denaturants, and photobleaching, and that it can be mutated to even longer wavelengths of excitation and emission. However, DsRed also shows slow and complex kinetics of maturation, proceeding via a green fluorescent protein (GFP)-like green intermediate to the final red species. DsRed also proves to be at least an obligate tetramer, two of which may weakly associate into an octamer (1). The present paper examines one of the most important fundamental unsolved questions about DsRed, namely the structure of the red chromophore and the mechanism by which it attains such long wavelengths. Matz et al. (2) speculated that ''an additional autocatalytic reaction, presumably inhibited in GFP, takes place during fluorophore maturation and leads to the extension of its conjugated -system.'' In an accompanying commentary, Tsien (3) raised the possibility that an amine side chain might attack the terminal carbonyl of the GFP chromophore to form an iminium cation somewhat analogous to that in rhodopsin. More recently, Terskikh et al.** suggested instead that ''the additional reaction is another cyclization within the backbone rather than attachment of a group derived from a neighboring side chain.'' All of these suggestions have been of generic reaction types rather than specific proposals of a detailed structure for the red chromophore.Our strategy relied critically on a point mutant, K83R, which remains almost entirely arrested at the green stage of maturation (1) and provides a reference standard for that intermediate...

the hydrogen of an acid such as HF approaches the peripheral of the benzene ring along an axis tilted toward the ring axis as predicted by the properties of the Laplacian distribution,1 to form a weak ir complex. In this complex, the bond path from the proton flicks from a carbon atom to a C-C bond with essentially no change in energy. The transformation of the complex into the protonated intermediate involves the charge rearrangements described above, and these are different from the pattern of charges found in the reactant molecules that determine the initial site of attack, and they involve much greater changes in the energy.Acknowledgment. Acknowledgment is made to the donors of the Petroleum Research Fund, administered by the American Chemical Society, for partial support of this research. AppendixTable AI summarizes the manner in which the substituents O", NH2, OH, F, CH3, CN, and N02 perturb the atomic populations of the benzene ring. The optimized geometries and corresponding energies of the protonated intermediates and protonated benzene, determined with basis sets 3-2lG, 4-3lG, 6-3lG, and 6-31G*, are tabulated in Tables AII-AVI.Registry No. [PhH]H+, 26812-57-7; [p-PhOH]H+, 53280-65-2; [m-PhOH]H+, H+, 57525-23-2; [m-PhF]H+, 74309-51-6; [p-PhCN]H+, 87176-59-8; [m-PhCN]H+, 87176-58-7; (CHj)2CHCH(CH3)C+(CH3)CH(CH3)CH(CH3)2, 120497-33-8; phenol, 108-95-2; fluorobenzene, 462-06-6; benzene, 71-43-2; benzonitrile, 100-47-0.