01741nas a2200217   4500008004100000245015100041210006900192260000800261490000800269520090500277100002101182700002101203700002301224700003001247700002201277700002101299700002501320700002901345700002101374856012801395       2010                        eng d00aNon-covalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers0 aNoncovalent interactions in extended systems described by the ef  cNOV0 v1143 aThe implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.1 aGhosh, Debashree1 aKosenkov, Dmytro1 aVanovschi, Vitalii1 aWilliams, Christopher, F.1 aHerbert, John, M.1 aGordon, Mark, S.1 aSchmidt, Michael, W.1 aSlipchenko, Lyudmila, V.1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/non-covalent-interactions-extended-systems-described-effective-fragment-potential-method01831nas a2200181   4500008004100000245010100041210006900142260000800211300001600219490000600235520117900241100002401420700002101444700001901465700001901484700002101503856012501524       2011                        eng d00aCorrection to what drives the redox properties of model green fluorescence protein chromophores?0 aCorrection to what drives the redox properties of model green fl  cOCT  a2695–26950 v23 a<p>We report the first experimental determination of the oxidation potentials E-ox(0). (relative to the standard hydrogen electrode, SHE) of model green fluorescent protein (GFP) chromophores. Para-, meta, and ortho-hydroxy (4-hydroxybenzylidene-2,3-dimethylimidazolinone, HBDI) and methoxy (MeOBDI) derivatives were studied. E-ox(0) of the three isomers in acetonitrile are -1.31, -1.52, and -1.39 V, respectively. Electronic structure calculations reproduce the observed differences between the isomers and reveal that E-ox(0) follows the ionization energies (IEs), that is, p-MeOBDI has the lowest IE (6.96 eV in the gas phase) due to resonance stabilization of its cation, whereas the resonance is detuned in m-MeOBDL resulting in more-negative E-ox(0). The observed meta and ortho effects in E-ox(0) are similar to the trends in pK(a). The effect of increased solvent polarity on absolute.E-ox(0) (and especially on para-meta-ortho differences) was found to be small. The redox properties of GFP chromophores are driven by their structure and can be correlated with IEs, which can be exploited in predicting the properties of other fluorescent protein chromophores.</p>1 aSolntsev, Kyril, M.1 aGhosh, Debashree1 aAmador, Adrian1 aJosowicz, Mira1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/correction-what-drives-redox-properties-model-green-fluorescence-protein-chromophores02027nas a2200169   4500008004100000245009800041210006900139260000800208300001400216490000800230520141600238100002101654700002101675700002901696700002101725856011101746       2011                        eng d00aEffect of solvation on the vertical ionization energy of thymine: from microhydration to bulk0 aEffect of solvation on the vertical ionization energy of thymine  cJUN  a6028-60380 v1153 aThe effect of hydration on the vertical ionization energy (VIE) of thymine was characterized using equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods. We considered several microsolvated clusters as well as thymine solvated in bulk water. The VIE in bulk water was computed by averaging over solvent-solute configurations obtained from equilibrium molecular dynamics trajectories at 300 K. The effect of microsolvation was analyzed and contrasted against the combined effect of the first solvation shell in bulk water. Microsolvation reduces the ionization energy (IE) by about 0.1 eV per water molecule, while the first solvation shell increases the IE by 0.1 eV. The subsequent solvation lowers the IE, and the bulk value of the solvent-induced shift of thymine's VIE is approximately -0.9 eV. The combined effect of the first solvation shell was explained in terms of specific solute-solvent interactions, which were investigated using model structures. The convergence of LE to the bulk value requires the hydration sphere of approximately 13.5 angstrom radius. The performance of the EOM-IP-CCSD/EFP scheme was benchmarked against full EOM-IP-CCSD using microhydrated structures. The errors were found to be less than 0.01-0.02 eV. The relative importance of the polarization and higher multipole moments in EFP model was also investigated.1 aGhosh, Debashree1 aIsayev, Olexandr1 aSlipchenko, Lyudmila, V.1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/effect-solvation-vertical-ionization-energy-thymine-microhydration-bulk01771nas a2200169   4500008004100000245008700041210006900128260000800197490000600205520117200211100002401383700002101407700001901428700001901447700002101466856011401487       2011                        eng d00aWhat drives the redox properties of model green fluorescence protein chromophores?0 aWhat drives the redox properties of model green fluorescence pro  cSEP0 v23 aWe report the first experimental determination of the oxidation potentials E-ox(0). (relative to the standard hydrogen electrode, SHE) of model green fluorescent protein (GFP) chromophores. Para-, meta, and ortho-hydroxy (4-hydroxybenzylidene-2,3-dimethylimidazolinone, HBDI) and methoxy (MeOBDI) derivatives were studied. E-ox(0) of the three isomers in acetonitrile are -1.31, -1.52, and -1.39 V, respectively. Electronic structure calculations reproduce the observed differences between the isomers and reveal that E-ox(0) follows the ionization energies (IEs), that is, p-MeOBDI has the lowest IE (6.96 eV in the gas phase) due to resonance stabilization of its cation, whereas the resonance is detuned in m-MeOBDL resulting in more-negative E-ox(0). The observed meta and ortho effects in E-ox(0) are similar to the trends in pK(a). The effect of increased solvent polarity on absolute.E-ox(0) (and especially on para-meta-ortho differences) was found to be small. The redox properties of GFP chromophores are driven by their structure and can be correlated with IEs, which can be exploited in predicting the properties of other fluorescent protein chromophores.1 aSolntsev, Kyril, M.1 aGhosh, Debashree1 aAmador, Adrian1 aJosowicz, Mira1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/what-drives-redox-properties-model-green-fluorescence-protein-chromophores01868nas a2200193   4500008004100000245017200041210006900213260000800282300001400290490000800304520112600312100002101438700001701459700001901476700001801495700002301513700002101536856011701557       2012                        eng d00aFirst-principle protocol for calculating ionization energies and redox potentials of solvatedmolecules and ions: theory and application to aqueous phenol and phenolate0 aFirstprinciple protocol for calculating ionization energies and   cJUN  a7269-72800 v1163 aThe effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP) and determined experimentally by valence photoemission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (Delta VIEs) are 0.66 and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8 +/- 0.1 and 7.1 +/- 0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using microsolvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 and 0.89 V, respectively; they agree well with experimental values.1 aGhosh, Debashree1 aRoy, Anirban1 aSeidel, Robert1 aWinter, Bernd1 aBradforth, Stephen1 aKrylov, Anna, I.  uhttps://library.ncl.res.in/content/first-principle-protocol-calculating-ionization-energies-and-redox-potentials02058nas 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-family01658nas a2200181   4500008004100000245011100041210006900152260000800221300001200229490000600241520099300247100002101240700001601261700002701277700002101304700001901325856013201344       2012                        eng d00aVUV Photoionization and Ab initio determination of the ionization energy of a gas-phasesugar (deoxyribose)0 aVUV Photoionization and Ab initio determination of the ionizatio  cJAN  a 97-1010 v33 aThe ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of alpha-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(+/- 0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (+/- 0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate.1 aGhosh, Debashree1 aGolan, Amir1 aTakahashi, Lynelle, K.1 aKrylov, Anna, I.1 aAhmed, Musahid  uhttps://library.ncl.res.in/content/vuv-photoionization-and-ab-initio-determination-ionization-energy-gas-phasesugar-deoxyribose02542nas a2200349   4500008004100000022001400041245008400055210006900139260006700208300001400275490000700289520144400296653003301740653001601773653001401789653001001803653000701813653001701820653002901837653001101866653001001877100002101887700002101908700002301929700001801952700001801970700001601988700002702004700002102031700002902052856011102081       2013                        eng d  a0192-865100aEffective fragment potential method in Q-CHEM: a guide for users and developers0 aEffective fragment potential method in QCHEM a guide for users a  a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcMAY  a1060-10700 v343 a<p>A detailed description of the implementation of the effective fragment potential (EFP) method in the Q-CHEM electronic structure package is presented. The Q-CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as HartreeFock, density functional theory, perturbation theory, and coupled-cluster methods, as well as with methods for electronically excited and open-shell species, for example, configuration interaction, time-dependent density functional theory, and equation-of-motion coupled-cluster models. In addition to the QM/EFP functionality, a fragment-only feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP module's workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q-CHEM's auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user-defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described. (c) 2013 Wiley Periodicals, Inc.</p>10aeffective fragment potential10aEFP library10ahybrid QM10aIQMOL10aMM10amodular code10anonempirical force field10aQ-CHEM10aWEBMO1 aGhosh, Debashree1 aKosenkov, Dmytro1 aVanovschi, Vitalii1 aFlick, Joanna1 aKaliman, Ilya1 aShao, Yihan1 aGilbert, Andrew, T. B.1 aKrylov, Anna, I.1 aSlipchenko, Lyudmila, V.  uhttps://library.ncl.res.in/content/effective-fragment-potential-method-q-chem-guide-users-and-developers-002796nas 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