@article {43246, title = {Introduction to the density matrix renormalization group ansatz in quantum chemistry}, journal = {Frontiers in Quantum Systems in Chemistry and Physics}, volume = {18}, year = {2008}, month = {JAN}, pages = {49-65}, type = {Proceedings Paper}, abstract = {The Density Matrix Renormalisation Group (DMRG) is an electronic structure method that has recently been applied to ab-initio quantum chemistry. Even at this early stage, it has enabled the solution of many problems that would previously have been intractable with any other method, in particular, multireference problems with very large active spaces. Historically, the DMRG was not originally formulated from a wavefunction perspective, but rather in a Renormalisation Group (RG) language. However, it is now realised that a wavefunction view of the DMRG provides a more convenient, and in some cases more powerful, paradigm. Here we provide an expository introduction to the DMRG ansatz in the context of quantum chemistry.}, author = {Chan, Garnet Kin-Lic and Dorando, Jonathan J. and Ghosh, Debashree and Hachmann, Johannes and Neuscamman, Eric and Wang, Haitao and Yanai, Takeshi} } @article {43245, title = {Orbital optimization in the density matrix renormalization group, with applications to polyenes and ss-carotene}, journal = {Journal of Chemical Physics}, volume = {128}, year = {2008}, month = {APR}, doi = {10.1063/1.2883976}, author = {Ghosh, Debashree and Hachmann, Johannes and Yanai, Takeshi and Chan, Garnet Kin-Lic} } @article {43242, title = {Accelerating convergence in iterative solution for large-scale complete active space self-consistent-field calculations}, journal = {International Journal of Quantum Chemistry}, volume = {109}, year = {2009}, month = {AUG}, pages = {2178-2190}, abstract = {An algorithm that accelerates the convergence of the iterative optimization of the complete active space self-consistent field (CASSCF) wavefunction so as to find a optimum solution in fewer macroiterations is described. The algorithm is oriented to large-scale CASSCF problems that are to be solved with a combination of density matrix renormalization group (DMRG) method for the configuration interaction (CI) process. The algorithm is based on the alternating (or two-step) CASSCF optimization in which the CI and molecular orbital (MO) parameters are optimized separately. Convergence ratio is improved by finding further optimized MOs from a linear extrapolation of the MO sets of the iteration history. The acceleration results in fewer diagonalizations in a total CASSCF calculation to save a considerable computational cost. The convergence performance is examined in a couple of realistic applications on SiC(3) and poly (phenyl)carbenes. For poly(phenyl)carbenes, the large-size CASSCF calculations with CAS(30e,30o) that entails full pi valence space as well as sp(2) orbital space of carbenes are performed by using the practical implementation of DMRG-CASSCF in conjunction with the acceleration technique. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 2178-2190, 2009}, doi = {10.1002/qua.22099}, author = {Yanai, Takeshi and Kurashige, Yuki and Ghosh, Debashree and Chan, Garnet Kin-Lic} } @article {43243, title = {Study of cumulant approximations to n-electron valence multireference perturbation theory}, journal = {Journal of Chemical Physics}, volume = {130}, year = {2009}, month = {MAY}, pages = {Article Number: 194107}, abstract = {We investigate the possibility of reducing the complexity of multireference perturbation theory through cumulant based approximations to the high-order density matrices that appear in such theories. Our test cases show that while the cumulant approximated forms are degraded in accuracy relative to the parent theory and exhibit intruder state problems that must be carefully handled, they may provide a route to a simple estimation of dynamic correlation when the parent perturbation theory is infeasible. Nonetheless, further work is clearly needed on better approximations to the denominators in the perturbation theory.}, doi = {10.1063/1.3132922}, author = {Zgid, Dominika and Ghosh, Debashree and Neuscamman, Eric and Chan, Garnet Kin-Lic} } @article {43241, title = {Non-covalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers}, journal = {Journal of Physical Chemistry A}, volume = {114}, year = {2010}, month = {NOV}, abstract = {The 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.}, author = {Ghosh, Debashree and Kosenkov, Dmytro and Vanovschi, Vitalii and Williams, Christopher F. and Herbert, John M. and Gordon, Mark S. and Schmidt, Michael W. and Slipchenko, Lyudmila V. and Krylov, Anna I.} } @article {43237, title = {Correction to what drives the redox properties of model green fluorescence protein chromophores?}, journal = {Journal of Physical Chemistry Letters}, volume = {2}, year = {2011}, month = {OCT}, pages = {2695{\textendash}2695}, chapter = {q}, abstract = {

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.

}, doi = {10.1021/jz201353v}, author = {Solntsev, Kyril M. and Ghosh, Debashree and Amador, Adrian and Josowicz, Mira and Krylov, Anna I.} } @article {43240, title = {Effect of solvation on the vertical ionization energy of thymine: from microhydration to bulk}, journal = {Journal of Physical Chemistry A}, volume = {115}, year = {2011}, month = {JUN}, pages = {6028-6038}, abstract = {The 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{\textquoteright}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.}, doi = {10.1021/jp110438c}, author = {Ghosh, Debashree and Isayev, Olexandr and Slipchenko, Lyudmila V. and Krylov, Anna I.} } @article {43239, title = {What drives the redox properties of model green fluorescence protein chromophores?}, journal = {Journal of Physical Chemistry Letters}, volume = {2}, year = {2011}, month = {SEP}, abstract = {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.}, doi = {10.1021/jz2011397}, author = {Solntsev, Kyril M. and Ghosh, Debashree and Amador, Adrian and Josowicz, Mira and Krylov, Anna I.} } @article {43235, title = {First-principle protocol for calculating ionization energies and redox potentials of solvatedmolecules and ions: theory and application to aqueous phenol and phenolate}, journal = {Journal of Physical Chemistry B}, volume = {116}, year = {2012}, month = {JUN}, pages = {7269-7280}, abstract = {The 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.}, doi = {10.1021/jp301925k}, author = {Ghosh, Debashree and Roy, Anirban and Seidel, Robert and Winter, Bernd and Bradforth, Stephen and Krylov, Anna I.} } @article {43236, title = {Toward understanding the redox properties of model chromophores from the greenfluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects}, journal = {Journal of Physical Chemistry B}, volume = {116}, year = {2012}, month = {OCT}, pages = {12398-12405}, abstract = {The 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.}, doi = {10.1021/jp305022t}, author = {Ghosh, Debashree and Acharya, Atanu and Tiwari, Subodh C. and Krylov, Anna I.} } @article {43234, title = {VUV Photoionization and Ab initio determination of the ionization energy of a gas-phasesugar (deoxyribose)}, journal = {Journal of Physical }, volume = {3}, year = {2012}, month = {JAN}, pages = { 97-101}, abstract = {The 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.}, doi = {10.1021/jz201446r}, author = {Ghosh, Debashree and Golan, Amir and Takahashi, Lynelle K. and Krylov, Anna I. and Ahmed, Musahid} } @article { ISI:000317082100007, title = {Effective fragment potential method in Q-CHEM: a guide for users and developers}, journal = {Journal of Computational Chemistry}, volume = {34}, number = {12}, year = {2013}, month = {MAY}, pages = {1060-1070}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

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{\textquoteright}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{\textquoteright}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.

}, keywords = {effective fragment potential, EFP library, hybrid QM, IQMOL, MM, modular code, nonempirical force field, Q-CHEM, WEBMO}, issn = {0192-8651}, doi = {10.1002/jcc.23223}, author = {Ghosh, Debashree and Kosenkov, Dmytro and Vanovschi, Vitalii and Flick, Joanna and Kaliman, Ilya and Shao, Yihan and Gilbert, Andrew T. B. and Krylov, Anna I. and Slipchenko, Lyudmila V.} } @article { ISI:000325392000050, title = {Perturbative approximations to single and double spin flip equation of motion coupled cluster singles doubles methods}, journal = {Journal of Chemical Physics}, volume = {139}, number = {12}, year = {2013}, month = {SEP}, pages = {124116}, publisher = {AMER INST PHYSICS}, address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA}, abstract = {

Spin flip equation of motion coupled cluster (EOM-SF-CC) can correctly treat situations involving electronic degeneracies or near degeneracies, e. g., bond breaking, di- and tri-radicals, etc. However, for large systems EOM-SF-CC (even in single and double excitations) is computationally prohibitively expensive. Therefore, earlier approximations to EOM-SF-CC methods such as spin flip configuration interaction singles with perturbative doubles (SF-CIS(D)) have been proposed. In this work, we present a new perturbative approximation to EOM-SF-CC, which has been found to be more accurate than SF-CIS(D). The capabilities, advantages, and timings of the new approach have been demonstrated considering the singlet-triplet gaps in di- and triradicals as well as bond breaking examples. The method is extended to double spin flip EOM-CC and its capabilities have been tested. (C) 2013 AIP Publishing LLC.

}, issn = {0021-9606}, doi = {10.1063/1.4821936}, author = {Dutta, Achintya Kumar and Pal, Sourav and Ghosh, Debashree} } @article { ISI:000344989500005, title = {Electrostatics determine vibrational frequency shifts in hydrogen bonded complexes}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, number = {46}, year = {2014}, month = {OCT}, pages = {25247-25250}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The red-shifts in the acetylenic C-H stretching vibration of C-H center dot center dot center dot X (X = O, N) hydrogen-bonded complexes increase with an increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the dispersion modulates the stabilization energy.

}, issn = {1463-9076}, doi = {10.1039/c4cp04617j}, author = {Dey, Arghya and Mondal, Sohidul Islam and Sen, Saumik and Ghosh, Debashree and Patwari, G. Naresh} } @article { ISI:000339367500022, title = {Ionization-induced tautomerization in cytosine and effect of solvation}, journal = {Journal of Physical Chemistry A}, volume = {118}, number = {28}, year = {2014}, month = {JUL}, pages = {5323-5332}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

The recent observation of excitation-induced tautomerization in gas-phase cytosine motivated us to investigate the possibility of facile tautomerization in ionized cytosine and the effect of solvation on the tautomerization barriers. The tautomerization mechanisms were characterized at the density functional theory (DFT)omega B97X-D and coupled-cluster singles and doubles (CCSD) levels of theory. Vertical and adiabatic ionization energies (VIEs and AIEs, respectively) of the tautomers of cytosine and the microsolvated species were calculated with the equation-of-motion ionization-potential coupled-cluster (EOM-IP-CCSD) method. We observed that, in microsolvated cytosine, the solvatochromic shifts of the VIEs can be both blue- and red-shifted depending on the tautomers. This is explained by the analysis of the charge dipole interactions between the cytosine and water molecules. We noticed that, upon ionization, gas-phase tautomerization barriers are reduced by 0-4 kcal/mol, whereas microsolvated (with one water) tautomerization barriers are reduced by 4-5 kcal/mol. We also investigated the tautomerization process in solvation using a continuum model with one active water molecule in the quantum mechanical region. We noticed that, even though bulk solvation has a significant effect on ionization energies, its effect on the ionization-induced tautomerization barrier is minimal.

}, issn = {1089-5639}, doi = {10.1021/jp503947d}, author = {Das, Tamal and Ghosh, Debashree} } @article { ISI:000334067400005, title = {Perturbative approximation to hybrid equation of motion coupled cluster/effective fragment potential method}, journal = {Journal of Chemical Physics}, volume = {140}, number = {9}, year = {2014}, month = {MAR}, pages = {094101}, publisher = {AMER INST PHYSICS}, address = {1305 WALT WHITMAN RD, STE 300, MELVILLE, NY 11747-4501 USA}, abstract = {

Hybrid quantum mechanics/molecular mechanics (QM/MM) methods provide an attractive way to closely retain the accuracy of the QM method with the favorable computational scaling of the MM method. Therefore, it is not surprising that QM/MM methods are being increasingly used for large chemical/biological systems. Hybrid equation of motion coupled cluster singles doubles/effective fragment potential (EOM-CCSD/EFP) methods have been developed over the last few years to understand the effect of solvents and other condensed phases on the electronic spectra of chromophores. However, the computational cost of this approach is still dominated by the steep scaling of the EOM-CCSD method. In this work, we propose and implement perturbative approximations to the EOM-CCSD method in this hybrid scheme to reduce the cost of EOM-CCSD/EFP. The timings and accuracy of this hybrid approach is tested for calculation of ionization energies, excitation energies, and electron affinities of microsolvated nucleic acid bases (thymine and cytosine), phenol, and phenolate. (C) 2014 AIP Publishing LLC.

}, issn = {0021-9606}, doi = {10.1063/1.4866838}, author = {Ghosh, Debashree} } @article {42933, title = {Advances in molecular quantum chemistry contained in the Q-Chem 4 program package}, journal = {Molecular Physics}, volume = {113}, year = {2015}, month = {JAN}, pages = {184-215}, abstract = {

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Moller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr-2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

}, author = {Shao, Yihan and Gan, Zhengting and Epifanovsky, Evgeny and Gilbert, Andrew T. B. and Wormit, Michael and Kussmann, Joerg and Lange, Adrian W. and Behn, Andrew and Deng, Jia and Feng, Xintian and Ghosh, Debashree} } @article { ISI:000363916400006, title = {Feasibility of ionization-mediated pathway for ultraviolet-induced melanin damage}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {42}, year = {2015}, month = {OCT}, pages = {13288-13293}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Melanin is the pigment found in human skin that is responsible for both photoprotection and photodamage. Recently there have been reports that greater photodamage of DNA occurs when cells containing melanin are irradiated with ultraviolet (UV) radiation, thus suggesting that the photoproducts of melanin cause DNA damage. Photoionization processes have also been implicated in the photodegradation of melanin. However, not much is known about the oxidation potential of melanin and its monomers. In this work we calculate the ionization energies of monomers, dimers, and few oligomers of eumelanin to estimate the threshold energy required for the ionization of eumelanin. We find that this threshold is within the UV-B region for eumelanin. We also look at the charge and spin distributions of the various ionized states of the monomers that are formed to understand which of the ionization channels might favor monomerization from a covalent dimer.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.5b08750}, author = {Mandal, Mukunda and Das, Tamal and Grewal, Baljinder K. and Ghosh, Debashree} } @article { ISI:000352270700029, title = {Singlet-triplet gaps in polyacenes: a delicate balance between dynamic and static correlations investigated by spin-flip methods}, journal = {Physical Chemistry Chemical Physics}, volume = {17}, number = {15}, year = {2015}, month = {MAR}, pages = {9849-9856}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Over the last few years people have been interested in the process of singlet fission, owing to its relevance to solar cell technology. The energetics of singlet fission is intimately related to singlet-triplet (ST) gaps and energies of singlet excited states. However, accurate calculations of ST gaps in polyacenes are complicated due to near degeneracies in the pi orbitals, and therefore, have been quite challenging. The spin-flip equation-of-motion coupled-cluster (SF-EOM-CC) and its perturbative approximation have been shown to correctly treat situations involving electronic degeneracies and near degeneracies. In this work, we use various spin-flip methods to benchmark the ST gaps of small polyacenes and show that the error in the ST gaps with respect to the experiment is small and does not increase appreciably with the system size. The diradical and polyradical character of the polyacene ground states increase with the system size. However, for the small polyacenes the open-shell character of the ground state is still small enough to be treated using single reference methods.

}, issn = {1463-9076}, doi = {10.1039/c5cp00214a}, author = {Ibeji, Collins U. and Ghosh, Debashree} } @article { ISI:000346235600046, title = {Spectroscopic and ab initio investigation of 2,6-difluorophenylacetylene-amine complexes: coexistence of C-H center dot center dot center dot N and lone-pair center dot center dot center dot pi complexes and intermolecular coulombic decay}, journal = {Physical Chemistry Chemical Physics}, volume = {17}, number = {1}, year = {2015}, month = {OCT}, pages = {434-443}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Binary complexes of 2,6-difluorophenylacetylene with methylamine, dimethylamine, trimethylamine and triethylamine were investigated using one colour resonant two photon ionization and infrared-optical double resonance spectroscopic techniques combined with high level ab initio calculations. All four amines form C-Ac-H center dot center dot center dot N hydrogen-bonded complexes. Additionally trimethylamine and triethylamine form complexes characterized by Lp center dot center dot center dot pi interactions, due to the electron deficient nature of the phenyl ring of 2,6-difluorophenylacetylene. The Lp center dot center dot center dot pi interacting structure of the 2,6-difluorophenylacetylenetrimethylamine complex is about 1.5 kJ mol(-1) higher in energy than the C-Ac-H center dot center dot center dot N hydrogen-bonded structure, which is the global minimum. Energy decomposition analysis indicates that the electrostatics and dispersion interactions favour the formation of C-Ac-H center dot center dot center dot N and Lp center dot center dot center dot pi complexes, respectively. Interestingly the C-Ac-H center dot center dot center dot N hydrogen-bonded complex of 2,6-difluorophenylacetylene-triethylamine showed a smaller shift in the acetylenic C-H stretching frequency than the 2,6-difluorophenylacetylene-trimethylamine complex. The observed fragmentation of the binary complexes of 2,6-difluorophenylacetylene with the four amines following resonant two-photon ionization can be explained on the basis of the intermolecular coulombic decay process.

}, issn = {1463-9076}, doi = {10.1039/c4cp03445g}, author = {Mondal, Sohidul Islam and Dey, Arghya and Sen, Saumik and Patwari, G. Naresh and Ghosh, Debashree} } @article { ISI:000371139400018, title = {Effect of sequence on the ionization of guanine in DNA}, journal = {Physical Chemistry Chemical Physics}, volume = {18}, number = {9}, year = {2016}, month = {MAR}, pages = {6526-6533}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected omega B97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.

}, issn = {1463-9076}, doi = {10.1039/c5cp07804k}, author = {Chakraborty, Rahul and Ghosh, Debashree} } @article { ISI:000376417400010, title = {Effect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {19}, year = {2016}, month = {MAY}, pages = {4410-4420}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Hybrid quantum mechanics/molecular mechanics (QM/MM) is applied to the fluorinated green fluorescent protein (GFP) chromophore (DFHBDI) in its deprotonated form to understand the solvatochromic shifts in its vertical detachment energy (VDE) and vertical excitation energy (VEE). This variant of the GFP chromophore becomes fluorescent in an RNA environment and has a wide range of applications in biomedical and biochemical fields. From microsolvation studies, we benchmark (with respect to full QM) the accuracy of our QM/MM calculations with effective fragment potential (EFP) as the MM method of choice. We show that while the solvatochromic shift in the VEE is minimal (0.1 eV blue shift) and its polarization component is only 0.03 eV, the effect of the solvent on the VDE is quite large (3.85 eV). We also show by accurate calculations on the solvatochromic shift of the VDE that polarization accounts for similar to 0.23 eV and therefore cannot be neglected. The effect of the counterions on the VDE of the deprotonated chromophore in solvation is studied in detail, and a charge-smearing scheme is suggested for charged chromophores.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.6b03723}, author = {Bose, Samik and Chakrabarty, Suman and Ghosh, Debashree} } @article { ISI:000373611700015, title = {Effects of the benzoxazole group on green fluorescent protein chromophore crystal structure and solid state photophysics}, journal = {Journal of Materials Chemistry C}, volume = {4}, number = {14}, year = {2016}, month = {DEC}, pages = {2793-2801}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Four benzoxazole-substituted GFP chromophores that differ by the length of their alkyl chain (from C1 to C12) were synthesized. In solution, the four compounds showed identical spectroscopic behavior, emitting blue light with moderate quantum yield. In the solid state, the butyl, pentyl and dodecyl derivatives strongly emitted orange light, while the methyl derivative was only weakly emissive. Based on the X-ray data and DFT calculations, emission in the solid state was explained by the formation of excimers. A very unusual {\textquoteleft}{\textquoteleft}hot-dog{\textquoteright}{\textquoteright}-type excimer was found for the dodecyl derivative, in which two overlapping chromophores are separated by an alkyl chain.

}, issn = {2050-7526}, doi = {10.1039/c5tc03776j}, author = {Ghodbane, Abdelhamid and Fellows, W. Brett and Bright, John R. and Ghosh, Debashree and Saffon, Nathalie and Tolbert, Laren M. and Fery-Forgues, Suzanne and Solntsev, Kyril M.} } @article { ISI:000379991000011, title = {Extension of the effective fragment potential method to macromolecules}, journal = {Journal of Physical Chemistry B}, volume = {120}, number = {27}, year = {2016}, month = {JUL}, pages = {6562-6574}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

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.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.6b04166}, author = {Gurunathan, Pradeep Kumar and Acharya, Atanu and Ghosh, Debashree and Kosenkov, Dmytro and Kaliman, Ilya and Shao, Yihan and Krylov, Anna I. and Slipchenko, Lyudmila V.} } @article {45654, title = {Theoretical study of the ground and excited state tautomersim in curcumin using DFT based methods}, journal = {Abstracts of Papers of the American Chemical Society}, volume = {252}, year = {2016}, month = {AUG }, type = {Article}, issn = {0065-7727}, author = {Grewal, Baljinder and Ghosh, Debashree} } @article {45720, title = {Electrostatic origin of the red solvatochromic shift of DFHBDI in RNA spinach}, journal = {Journal of Physical Chemistry B}, volume = {121}, year = {2017}, month = {MAY}, pages = {4790-4798}, type = {Article}, abstract = {

Interactions with the environment tune the spectral properties of biological chromophores, e.g., fluorescent proteins. Understanding the relative contribution of the various types of noncovalent interactions in the spectral shifts can provide rational design principles toward developing new fluorescent probes. In this work, we investigate the origin of the red shift in the absorption spectra of the difluoro hydroxybenzylidene dimethyl imidazolinone (DFHBDI) chromophore in RNA spinach as compared to the aqueous solution. We systematically decompose the effects of various components of interactions, namely, stacking, hydrogen bonding, and long-range electrostatics, in order to elucidate the relative role of these interactions in the observed spectral behavior. We find that the absorption peak of DFHBDI is red-shifted by similar to 0.35 eV in RNA relative to the aqueous solution. Earlier proposals from Huang and co-workers have implicated the stacking interactions between DFHBDI and nucleic acid bases to be the driving force behind the observed red shift. In contrast, our findings reveal that the long-range electrostatic interactions between DFHBDI and negatively charged RNA. make the most significant contribution. Moreover, we notice that the opposing electrostatic fields due to the RNA backbone and the polarized water molecules around the RNA give rise to the resultant red shift. Our results emphasize the effect of strong heterogeneity in the various environmental factors that might be competing with each other.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.7b02445}, author = {Bose, Samik and Chakrabarty, Suman and Ghosh, Debashree} } @article {42931, title = {Hybrid equation-of-motion coupled-cluster/effective fragment potential method: a route toward understanding photoprocesses in the condensed phase}, journal = {Journal of Physical Chemistry A}, volume = {121}, year = {2017}, month = {DEC}, pages = {741-752}, type = {Article}, abstract = {

The prediction of accurate solvatochromic shifts to the electronic excited states of chromophores is a challenge, especially in the complex biological phase, due to the importance of long-range electrostatic interactions. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are generally employed for the calculation of quantum mechanical properties in complex systems. To be predictive, there is need for an accurate quantum mechanical method that can depict the charge transfer states correctly and incorporate higher than single excited determinants in its linear response ansatz. On the contrary, for the correct depiction of the environment interactions (MM region), one needs to account for polarizability in a balanced manner. These two challenges are successfully addressed by the recently developed hybrid quantum mechanical/effective fragment potential (QM/EFP) methods, with equation-of-motion coupled-cluster (EOM-CC) as the QM method of choice. The result is an efficient method to estimate excitation energy, ionization energy, electron affinity, and redox potential in the condensed phase. It has further been extended to biological systems.

}, doi = {10.1021/acs.jpca.6b08263}, author = {Ghosh, Debashree} } @article {43777, title = {Interaction energy driven biased sampling technique: a faster route to ionization spectra in condensed phase}, journal = {Journal of Computational Chemistry}, volume = {38}, year = {2017}, month = {OCT}, pages = {2248-2257}, abstract = {We introduce a computationally efficient approach for calculating spectroscopic properties, such as ionization energies (IEs) in the condensed phase. Discrete quantum mechanical/molecular mechanical (QM/MM) approaches for spectroscopic properties in a dynamic system, such as aqueous solution, need a large sample space to obtain converged estimates, especially for the cases where particle (electron) number is not conserved, such as IEs or electron affinities (EAs). We devise a biased sampling technique based on an approximate estimate of interaction energy between the solute and solvent, that accelerates the convergence and therefore, reduces the computational cost significantly. The approximate interaction energy also provides a good measure of the spectral width of the chromophores in the condensed phase. This technique has been tested and benchmarked for (i) phenol, (ii) HBDI anion (hydroxybenzylidene dimethyl imidazolinone), and (iii) thymine in water. (c) 2017 Wiley Periodicals, Inc.}, doi = {10.1002/jcc.24875}, author = {Bose, Samik and Ghosh, Debashree} } @article {45676, title = {Multiscale modelling: hybrid quantum mechanics/molecular mechanics as an example and some recent developments}, journal = {Current Science}, volume = {112 }, year = {2017}, month = {APR}, pages = {1455-1462}, type = {Article}, abstract = {Most of the physical phenomena are multiscale in nature and therefore, to depict it properly one requires multiscale modelling techniques, i.e. physical models that are accurate over multiple length and time scales. The seminal work by Warshel and Levitt marks the beginning of hybrid quantum mechanics/molecular mechanics (QM/MM) method as a successful strategy towards the understanding of chemistry and physics in condensed phases and especially in biological systems. Recently, these methods have been extended to problems such as light-matter interaction, where the QM sub-system is excited from the ground to the excited states. The MM environment provides a field that changes the potential energy landscape of both the ground and excited states in a distinctly different way. In this review, we discuss the general strategy of multiscale modelling with emphasis on hybrid QM/MM and the recent developments in excited state QM/MM methods.}, doi = {10.18520/cs/v112/i07/1455-1462}, author = {Ghosh, Debashree} } @article {43817, title = {Nature of selenium hydrogen bonding: gas phase spectroscopy and quantum chemistry calculations}, journal = {Physical chemistry Chemical physics}, volume = {19}, year = {2017}, month = {SEP}, pages = {24179-24187}, type = {Article}, abstract = {

Subsequent to the recent re-definition of hydrogen bonding by the IUPAC committee, there has been a growing search for finding the presence of this ever interesting non-covalent interaction between a hydrogen atom in an X-H group and any other atom in the periodic table. In recent gas phase experiments, it has been observed that hydrogen bonding interactions involving S and Se are of similar strength to those with an O atom. However, there is no clear explanation for the unusual strength of this interaction in the case of hydrogen bond acceptors which are not conventional electronegative atoms. In this work, we have explored the nature of Se hydrogen bonding by studying indole...dimethyl selenide (indmse) and phenol...dimethyl selenide (phdmse) complexes using gas phase IR spectroscopy and quantum chemistry calculations. We have found through various energy decomposition analysis (EDA) methods and natural bond orbital (NBO) calculations that, along with electrostatics and polarization, charge transfer interactions are important to understand Se/S hydrogen bonding and there is a delicate balance between the various interactions that plays the crucial role rather than a single component of the interaction energy. An in-depth understanding of this type of non-covalent interaction has immense significance in biology as amino acids containing S and Se are widely present in proteins and hence hydrogen bonding interactions involving S and Se atoms contribute to the folding of proteins.

}, keywords = {Center-Dot-O, Clusters, Co-Ordination, Complexes, intermolecular interactions, Proteins, Replacement, spectra, Strength, Sulfur}, issn = {1463-9076}, doi = {10.1039/c7cp05265k}, author = {Mishra, Kamal K. and Singh, Santosh K. and Ghosh, Paulami and Ghosh, Debashree and Das, Aloke} } @article {43866, title = {Unprecedented solvent induced inter-conversion between monomeric and dimeric silylene-zinc iodide adducts}, journal = {Dalton Transaction }, volume = {46}, year = {2017}, month = {SEP}, chapter = {11418-11424}, abstract = {

Usually, when a silylene reacts with a transition metal Lewis acid, it forms an adduct which could be either monomeric or dimeric. However, we present here that a silylene, [PhC(NtBu)(2)SiN(SiMe3)(2)] can form both monomeric [PhC(NtBu)(2)Si{N(SiMe3)(2)} -\> ZnI2]center dot THF (1) and dimeric [{PhC(NtBu)(2)}(N(SiMe3)(2))SiZnI,(mu-I)](2) (2) adducts upon reaction with ZnI2. The formation of 1 and 2 relies upon the solvent used for the reaction or crystallization. When the crystallization is carried out in THF complex 1 is formed, however, when the reaction and crystallization are performed in acetonitrile complex 2 is obtained. Both 1 and 2 were structurally authenticated and the nature of the Si-Zn bond in these complexes was determined by quantum chemical calculations. In addition, a spontaneous inter-conversion between 1 and 2 just by changing the solvents has been also observed; a feature presently not known for silylene-transition metal Lewis adducts.

}, keywords = {Bis(Silylene ), Carbene Complexes, Crystal -structure Determination, Dative bond, Lewis acid base reaction, Ligands, Main- group compounds, Reactivity, Silicon(II) Bis(Trimethylsilyl)Amide; Carbonyl-Complexes}, issn = {1477-9226}, doi = {10.1039/c7dt01823a}, author = {Yadav, Sandeep and Sangtani, Ekta and Dhawan, Diksha and Gonnade, Rajesh G. and Ghosh, Debashree and Sen, Sakya S.} } @article {45360, title = {Machine learning prediction of interaction energies in rigid water clusters}, journal = {Physical Chemistry Chemical Physics }, volume = {20}, year = {2018}, month = {SEP}, pages = {22987-22996}, type = {Article}, abstract = {Classical force fields form a computationally efficient avenue for calculating the energetics of large systems. However, due to the constraints of the underlying analytical form, it is sometimes not accurate enough. Quantum mechanical (QM) methods, although accurate, are computationally prohibitive for large systems. In order to circumvent the bottle-neck of interaction energy estimation of large systems, data driven approaches based on machine learning (ML) have been employed in recent years. In most of these studies, the method of choice is artificial neural networks (ANN). In this work, we have shown an alternative ML method, support vector regression (SVR), that provides comparable accuracy with better computational efficiency. We have further used many body expansion (MBE) along with SVR to predict interaction energies in water clusters (decamers). In the case of dimer and trimer interaction energies, the root mean square errors (RMSEs) of the SVR based scheme are 0.12 kcal mol(-1) and 0.34 kcal mol(-1), respectively. We show that the SVR and MBE based scheme has a RMSE of 2.78\% in the estimation of decamer interaction energy against the parent QM method in a computationally efficient way.}, doi = {10.1039/c8cp03138j}, author = {Bose, Samik and Dhawan, Diksha and Nandi, Sutanu and Sarkar, Ram Rup and Ghosh, Debashree} }