02058nas a2200169   4500008004100000245018900041210006900230260000800299300001600307490000800323520134500331100002101676700001901697700002301716700002101739856012801760       2012                        eng d00aToward understanding the redox properties of model chromophores from the greenfluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects0 aToward understanding the redox properties of model chromophores   cOCT  a12398-124050 v1163 aThe redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E-red(0)) of the anionic (Chr(center dot)/Chr(-)) and neutral (Chr(+center dot)/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and -0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.1 aGhosh, Debashree1 aAcharya, Atanu1 aTiwari, Subodh, C.1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/toward-understanding-redox-properties-model-chromophores-greenfluorescent-protein-family02796nas a2200229   4500008004100000022001400041245007500055210006900130260007100199300001400270490000800284520199800292100003102290700001902321700002102340700002102361700001802382700001602400700002102416700002902437856010002466       2016                        eng d  a1520-610600aExtension of the effective fragment potential method to macromolecules0 aExtension of the effective fragment potential method to macromol  a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcJUL  a6562-65740 v1203 a<p>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 C-alpha-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the C-alpha-C and C-alpha-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.</p>1 aGurunathan, Pradeep, Kumar1 aAcharya, Atanu1 aGhosh, Debashree1 aKosenkov, Dmytro1 aKaliman, Ilya1 aShao, Yihan1 aKrylov, Anna, I.1 aSlipchenko, Lyudmila, V.  uhttps://library.ncl.res.in/content/extension-effective-fragment-potential-method-macromolecules