The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

We present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters.

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Equation of motion coupled cluster calculations were performed on various structures of OH in clusters with one, two, three, and four water molecules to determine the energies of valence and charge transfer states. Motivation for these calculations is to understand the absorption spectrum of OH in water. Previous calculations on these species have confirmed that the longer wavelength transition observed is due to the A((2)∑) ← X((2)∏) valence transition, while the shorter wavelength transition is due to a charge-transfer from H2O to OH. While these previous calculations identified the lowest energy charge-transfer state, our calculations have included sufficient states to identify additional solvent-to-solute charge transfer states. The minimum energy structures of the clusters were determined by application of the Monte Carlo technique to identify candidate cluster structures, followed by optimization at the level of second-order Møller-Plesset perturbation theory. Calculations were performed on two structures of OH-H2O, three structures of OH-(H2O)2, four structures of OH-(H2O)3, and seven structures of OH-(H2O)4. Confirming previous calculations, as the number of water molecules increases, the energies of the excited valence and charge-transfer states decrease; however, the total number of charge-transfer states increases with the number of water molecules, suggesting that in the limit of OH in liquid water, the charge-transfer states form a band.

The propensity of carboxyl⋯pyridyl synthon is more than carboxyl⋯pyridyl N-oxide synthon, but carboxyl⋯pyridyl N-oxide synthon forms shorter hydrogen bond than carboxyl⋯pyridyl synthon. Carboxyl⋯pyridyl N-oxide synthon containing systems might show better solubility than the corresponding carboxyl⋯pyridyl synthon containing systems.