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A simulation study of DPDPE in sodium chloride solution has been performed and compared with previous simulations using a different interaction potential for the ions. Both global thermodynamics as well as a characterization of association to DPDPE have been calculated. We show that the parameters used for the ions have a profound effect on the association to the peptide in 1M NaCl. The observed differences suggest that individual associations in these and previous simulations are sensitive to parameters. © 2001 John Wiley & Sons, Inc. Biopolymers (Pept Sci) 60: 134–152, 2001

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In order to quantify specific ion effects, a simulation study of bis(penicllamine) enkephalin, also known as DPDPE, has been performed in aqueous ammonium chloride solution and has been compared to a previous simulation of DPDPE in aqueous sodium chloride solution. Global thermodynamics have been calculated for a model system and the solution environment around DPDPE has been characterized. Associations of ions with DPDPE have been investigated. The observed differences between sodium chloride solution and ammonium chloride solution suggest that individual cations affect the solvation and peptide binding properties of a given anion.

We report the calculated characteristics of nonnatural triplex-forming oligonucleotide (TFO) bases recognizing base-pair reversals (TA-->AT) in a double-helical DNA sequence. Ab initio and molecular mechanics calculations have been carried out to characterize the geometric and energetic consequences at the base-pair reversal sites. We have estimated the free energies of solvation of the natural and proposed bases by solving the linearized Poisson-Boltzmann equation. The calculations indicate that the proposed TFO bases should bind with some specificity to the duplex. Implications of the strategy used in the context of molecular biology is discussed.