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Carter-Fenk K, Mundy CJ, Herbert JM. Natural Charge-Transfer Analysis: Eliminating Spurious Charge-Transfer States in Time-Dependent Density Functional Theory via Diabatization, with Application to Projection-Based Embedding. J Chem Theory Comput 2021; 17:4195-4210. [PMID: 34189922 DOI: 10.1021/acs.jctc.1c00412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For many types of vertical excitation energies, linear-response time-dependent density functional theory (LR-TDDFT) offers a useful degree of accuracy combined with unrivaled computational efficiency, although charge-transfer excitation energies are often systematically and dramatically underestimated, especially for large systems and those that contain explicit solvent. As a result, low-energy electronic spectra of solution-phase chromophores often contain tens to hundreds of spurious charge-transfer states, making LR-TDDFT needlessly expensive in bulk solution. Intensity borrowing by these spurious states can affect intensities of the valence excitations, altering electronic bandshapes. At higher excitation energies, it is difficult to distinguish spurious charge-transfer states from genuine charge-transfer-to-solvent (CTTS) excitations. In this work, we introduce an automated diabatization that enables fast and effective screening of the CTTS acceptor space in bulk solution. Our procedure introduces "natural charge-transfer orbitals" that provide a means to isolate orbitals that are most likely to participate in a CTTS excitation. Projection of these orbitals onto solvent-centered virtual orbitals provides a criterion for defining the most important solvent molecules in a given excitation and be used as an automated subspace selection algorithm for projection-based embedding of a high-level description of the CTTS state in a lower-level description of its environment. We apply this method to an ab initio molecular dynamics trajectory of I-(aq) and report the lowest-energy CTTS band in the absorption spectrum. Our results are in excellent agreement with the experiment, and only one-third of the water molecules in the I-(H2O)96 simulation cell need to be described with LR-TDDFT to obtain excitation energies that are converged to <0.1 eV. The tools introduced herein will improve the accuracy, efficiency, and usability of LR-TDDFT in solution-phase environments.
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Affiliation(s)
- Kevin Carter-Fenk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Marin TW, Janik I, Bartels DM, Chipman DM. Failure of molecular dynamics to provide appropriate structures for quantum mechanical description of the aqueous chloride ion charge-transfer-to-solvent ultraviolet spectrum. Phys Chem Chem Phys 2021; 23:9109-9120. [PMID: 33885094 DOI: 10.1039/d1cp00930c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lowest band in the charge-transfer-to-solvent ultraviolet absorption spectrum of aqueous chloride ion is studied by experiment and computation. Interestingly, the experiments indicate that at concentrations up to at least 0.25 M, where calculations indicate ion pairing to be significant, there is no notable effect of ionic strength on the spectrum. The experimental spectra are fitted to aid comparison with computations. Classical molecular dynamic simulations are carried out on dilute aqueous Cl-, Na+, and NaCl, producing radial distribution functions in reasonable agreement with experiment and, for NaCl, clear evidence of ion pairing. Clusters are extracted from the simulations for quantum mechanical excited state calculations. Accurate ab initio coupled-cluster benchmark calculations on a small number of representative clusters are carried out and used to identify and validate an efficient protocol based on time-dependent density functional theory. The latter is used to carry out quantum mechanical calculations on thousands of clusters. The resulting computed spectrum is in excellent agreement with experiment for the peak position, with little influence from ion pairing, but is in qualitative disagreement on the width, being only about half as wide. It is concluded that simulation by classical molecular dynamics fails to provide an adequate variety of structures to explain the experimental CTTS spectrum of aqueous Cl-.
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Affiliation(s)
- Timothy W Marin
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, IL 60532, USA
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3
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Zhao L, Neuscamman E. Excited state mean-field theory without automatic differentiation. J Chem Phys 2020; 152:204112. [DOI: 10.1063/5.0003438] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Luning Zhao
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Eric Neuscamman
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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4
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Jana G, Jha R, Pan S, Chattaraj PK. Microsolvation of lithium–phosphorus double helix: a DFT study. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2462-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Troian-Gautier L, Turlington MD, Wehlin SAM, Maurer AB, Brady MD, Swords WB, Meyer GJ. Halide Photoredox Chemistry. Chem Rev 2019; 119:4628-4683. [PMID: 30854847 DOI: 10.1021/acs.chemrev.8b00732] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Halide photoredox chemistry is of both practical and fundamental interest. Practical applications have largely focused on solar energy conversion with hydrogen gas, through HX splitting, and electrical power generation, in regenerative photoelectrochemical and photovoltaic cells. On a more fundamental level, halide photoredox chemistry provides a unique means to generate and characterize one electron transfer chemistry that is intimately coupled with X-X bond-breaking and -forming reactivity. This review aims to deliver a background on the solution chemistry of I, Br, and Cl that enables readers to understand and utilize the most recent advances in halide photoredox chemistry research. These include reactions initiated through outer-sphere, halide-to-metal, and metal-to-ligand charge-transfer excited states. Kosower's salt, 1-methylpyridinium iodide, provides an early outer-sphere charge-transfer excited state that reports on solvent polarity. A plethora of new inner-sphere complexes based on transition and main group metal halide complexes that show promise for HX splitting are described. Long-lived charge-transfer excited states that undergo redox reactions with one or more halogen species are detailed. The review concludes with some key goals for future research that promise to direct the field of halide photoredox chemistry to even greater heights.
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Affiliation(s)
- Ludovic Troian-Gautier
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Michael D Turlington
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Sara A M Wehlin
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Andrew B Maurer
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Matthew D Brady
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Wesley B Swords
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Gerald J Meyer
- Department of Chemistry , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
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6
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Dubosq C, Zanuttini D, Gervais B. RASPT2 Analysis of the F–(H2O)n=1–7 and OH–(H2O)n=1–7 CTTS States. J Phys Chem A 2018; 122:7033-7041. [DOI: 10.1021/acs.jpca.8b04970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Dubosq
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR 6252, BP 5133, F-14070 Caen Cedex 05, France
| | - D. Zanuttini
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR 6252, BP 5133, F-14070 Caen Cedex 05, France
| | - B. Gervais
- Normandie University, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, UMR 6252, BP 5133, F-14070 Caen Cedex 05, France
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7
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Shi R, Wang P, Tang L, Huang X, Chen Y, Su Y, Zhao J. Structures and Spectroscopic Properties of F -(H 2O) n with n = 1-10 Clusters from a Global Search Based On Density Functional Theory. J Phys Chem A 2018; 122:3413-3422. [PMID: 29546760 DOI: 10.1021/acs.jpca.7b08872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a genetic algorithm incorporated in density functional theory, we explore the ground state structures of fluoride anion-water clusters F-(H2O) n with n = 1-10. The F-(H2O) n clusters prefer structures in which the F- anion remains at the surface of the structure and coordinates with four water molecules, as the F-(H2O) n clusters have strong F--H2O interactions as well as strong hydrogen bonds between H2O molecules. The strong interaction between the F- anion and adjacent H2O molecule leads to a longer O-H distance in the adjacent molecule than in an individual water molecule. The simulated infrared (IR) spectra of the F-(H2O)1-5 clusters obtained via second-order vibrational perturbation theory (VPT2) and including anharmonic effects reproduce the experimental results quite well. The strong interaction between the F- anion and water molecules results in a large redshift (600-2300 cm-1) of the adjacent O-H stretching mode. Natural bond orbital (NBO) analysis of the lowest-energy structures of the F-(H2O)1-10 clusters illustrates that charge transfer from the lone pair electron orbital of F- to the antibonding orbital of the adjacent O-H is mainly responsible for the strong interaction between the F- anion and water molecules, which leads to distinctly different geometric and vibrational properties compared with neutral water clusters.
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Affiliation(s)
- Ruili Shi
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams , Dalian University of Technology, Ministry of Education , Dalian 116024 , China
| | - Pengju Wang
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams , Dalian University of Technology, Ministry of Education , Dalian 116024 , China
| | - Lingli Tang
- College of Science , Dalian Minzu University , Dalian 116600 , China
| | - Xiaoming Huang
- School of Ocean Science and Technology , Dalian University of Technology , Panjin Campus, Panjin 124221 , China
| | - Yonggang Chen
- Network and Information Center , Dalian University of Technology , Dalian 116024 , China
| | - Yan Su
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams , Dalian University of Technology, Ministry of Education , Dalian 116024 , China
| | - Jijun Zhao
- Key Laboratory of Materials Modification by Laser, Ion and Electron Beams , Dalian University of Technology, Ministry of Education , Dalian 116024 , China
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8
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Ge Q, Mao Y, Head-Gordon M. Energy decomposition analysis for exciplexes using absolutely localized molecular orbitals. J Chem Phys 2018; 148:064105. [DOI: 10.1063/1.5017510] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Qinghui Ge
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Yuezhi Mao
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA
- Chemical Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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9
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Zilberg S, Mizrahi A, Meyerstein D, Kornweitz H. Carbonate and carbonate anion radicals in aqueous solutions exist as CO3(H2O)62− and CO3(H2O)6˙− respectively: the crucial role of the inner hydration sphere of anions in explaining their properties. Phys Chem Chem Phys 2018; 20:9429-9435. [DOI: 10.1039/c7cp08240a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An effort to reproduce the physical properties of CO32− and CO3˙− in water proves that one has to include an inner hydration sphere of six water molecules for both anions.
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Affiliation(s)
| | - Amir Mizrahi
- Chemistry Department
- Ben-Gurion University
- Beer-Sheva
- Israel
| | - Dan Meyerstein
- Chemical Sciences Department
- Ariel University
- Ariel
- Israel
- Chemistry Department
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10
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Wen H, Huang T, Liu YR, Jiang S, Peng XQ, Miao SK, Wang CY, Hong Y, Huang W. Structure, temperature effect and bonding order analysis of hydrated bromide clusters. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.09.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Uchiho Y, Goto Y, Kamahori M, Aota T, Morisaki A, Hosen Y, Koda K. Far-ultraviolet absorbance detection of sugars and peptides by high-performance liquid chromatography. J Chromatogr A 2015; 1424:86-91. [DOI: 10.1016/j.chroma.2015.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/20/2015] [Accepted: 11/01/2015] [Indexed: 10/22/2022]
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12
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Mondal S, Teja AU, Singh PC. Theoretical Study on the Microhydration of Atmospherically Important Carbonyl Sulfide in Its Neutral and Anionic Forms: Bridging the Gap between the Bulk and Finite Size Microhydrated Cluster. J Phys Chem A 2015; 119:3644-52. [DOI: 10.1021/acs.jpca.5b01638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Avula Uday Teja
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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13
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GUHA SATYAJIT, NEOGI SOUMYAGANGULY, CHAUDHURY PINAKI. Study of structure and spectroscopy of water–hydroxide ion clusters: A combined simulated annealing and DFT-based approach. J CHEM SCI 2014. [DOI: 10.1007/s12039-014-0613-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Dolgounitcheva O, Zakrzewski V, Streit L, Ortiz J. Microsolvation effects on the electron binding energies of halide anions. Mol Phys 2014. [DOI: 10.1080/00268976.2013.812756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Affiliation(s)
- Dilip K. Maity
- Theoretical
Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
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16
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Dolgounitcheva O, Zakrzewski VG, Ortiz JV. Assignment of photoelectron spectra of halide–water clusters: Contrasting patterns of delocalization in Dyson orbitals. J Chem Phys 2013; 138:164317. [DOI: 10.1063/1.4802251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- O Dolgounitcheva
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
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17
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Das R, Bandaru S, D’mello VC, Chattaraj PK. Effect of microsolvation on hydrogen trapping potential of metal ions. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Neogi SG, Chaudhury P. Structure and spectroscopic aspects of water-halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods. J Comput Chem 2012; 34:471-91. [DOI: 10.1002/jcc.23156] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/01/2012] [Accepted: 09/07/2012] [Indexed: 01/17/2023]
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19
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Kolaski M, Cho SJ. Monohydrated Sulfuric and Phosphoric Acids with Different Hydrogen Atom Orientations: DFT and Ab initio Study. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.6.1998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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20
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Pathak AK. Normal modes for probing the local solvation environment of nitrate anion during step wise hydration: A theoretical study. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.02.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Prakash M, Gopalsamy K, Subramanian V. Studies on the structure, stability, and spectral signatures of hydride ion-water clusters. J Chem Phys 2012; 135:214308. [PMID: 22149793 DOI: 10.1063/1.3663708] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The gas-phase structure, stability, spectra, and electron density topography of H(-)W(n) clusters (where n = 1-8) have been calculated using coupled-cluster CCSD(T) and Møller-Plesset second-order perturbation (MP2) theory combined with complete basis set (CBS) approaches. The performance of various density functional theory (DFT) based methods such as B3LYP, M05-2X, M06, M06-L, and M06-2X using 6-311++G(d,p), and aug-cc-pVXZ (aVXZ, where X = D, T, and Q) basis sets has also been assessed by considering values calculated using CCSD(T)/CBS limit as reference. The performance of the functionals has been ranked based on the mean signed/unsigned error. The comparison of geometrical parameters elicits that the geometrical parameters predicted by B3LYP/aVTZ method are in good agreement with those values obtained at MP2/aVTZ level of theory. Results show that M05-2X functional outperform other functionals in predicting the energetics when compared to CCSD(T)/CBS value. On the other hand, values predicted by M06-2X, and M06 methods, are closer to those values obtained from MP2/CBS approach. It is evident from the calculations that H(-)W(n) (where n = 5-8) clusters adopt several interesting structural motifs such as pyramidal, prism, book, Clessidra, cubic, cage, and bag. The important role played by ion-water (O-H···H(-)) and water-water (O-H···O) interactions in determining the stability of the clusters has also been observed. Analysis of the results indicates that the most stable cluster is made up of minimum number of O-H···H(-) interaction in conjugation with the maximum number of O-H···O interactions. The Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses has also been carried out to characterize the nature of interactions between hydride ion and water molecules. It can be observed from the vibrational spectra of H(-)W(n) clusters, the stretching frequencies involving ion-water interaction always exhibit larger redshift and intensities than that of water-water (inter solvent) interactions.
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Affiliation(s)
- M Prakash
- Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai 600 020, India
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22
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Min SK, Cho Y, Kim KS. Efficient electron dynamics with the planewave-based real-time time-dependent density functional theory: Absorption spectra, vibronic electronic spectra, and coupled electron-nucleus dynamics. J Chem Phys 2011; 135:244112. [DOI: 10.1063/1.3671952] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Pathak AK. Structure and photoelectron spectral properties of I(-)·nCO2 clusters: an ab initio study. Chemphyschem 2011; 12:2641-5. [PMID: 21954006 DOI: 10.1002/cphc.201100436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Indexed: 11/07/2022]
Abstract
Structures and photoelectron spectral properties of I(-)·nCO(2) (n=1-7) clusters are presented at the level of second-order Møller-Plesset perturbation theory with relativistic corrections. Triple split-valence 6-311++G(d,p) basis set functions are employed herein. It is observed that the CO(2) molecules approach the I(-) anion from one side in all the clusters and that I(-)·nCO(2) clusters prefer the surface structure. The calculated vertical detachment energy of these clusters is in excellent agreement with the reported experimentally measured values (within 4%). Efforts are also made to extract vertical detachment energy of large size of clusters, including the bulk. The extracted vertical detachment energy values for larger clusters (n=8-13) by employing the microscopic theory-based expression are also close (within 4%) to that of the experimentally measured values.
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Affiliation(s)
- Arup K Pathak
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai, India.
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24
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Park SW, Kim CW, Lee JH, Shim G, Kim KS. Comparison of Arsenic Acid with Phosphoric Acid in the Interaction with a Water Molecule and an Alkali/Alkaline-Earth Metal Cation. J Phys Chem A 2011; 115:11355-61. [DOI: 10.1021/jp2051245] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Sung Woo Park
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Chang Woo Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Ji Hyun Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Giwoong Shim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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25
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Kołaski M, Zakharenko AA, Karthikeyan S, Kim KS. Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study. J Chem Theory Comput 2011; 7:3447-59. [DOI: 10.1021/ct100428z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maciej Kołaski
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Aleksey A. Zakharenko
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - S. Karthikeyan
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, 790-784 Pohang, South Korea
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26
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Pathak AK. Connecting finite size charge-transfer-to-solvent energy to the bulk: A general microscopic theory. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Pham VT, Penfold TJ, van der Veen RM, Lima F, El Nahhas A, Johnson SL, Beaud P, Abela R, Bressler C, Tavernelli I, Milne CJ, Chergui M. Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution. J Am Chem Soc 2011; 133:12740-8. [DOI: 10.1021/ja203882y] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Van-Thai Pham
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas J. Penfold
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie Et Biochimie Computationnelles, ISIC-FSB, CH-1015 Lausanne, Switzerland
| | - Renske M. van der Veen
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Frederico Lima
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Amal El Nahhas
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Steve L. Johnson
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Paul Beaud
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Rafael Abela
- Swiss Light Source, Paul-Scherrer-Institut, CH-5232 PSI-Villigen, Switzerland
| | - Christian Bressler
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Chimie Et Biochimie Computationnelles, ISIC-FSB, CH-1015 Lausanne, Switzerland
| | - Christopher J. Milne
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Majed Chergui
- Ecole Polytechnique Fédérale de Lausanne, Laboratoire de Spectroscopie Ultrarapide, ISIC-FSB, Station 6, CH-1015 Lausanne, Switzerland
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Chen Y, Pan X, Yan H, Tan N. Multiple hydrogen-bonding interactions between macrocyclic triurea and F−, Cl−, Br−, I− and NO3−: a theoretical investigation. Phys Chem Chem Phys 2011; 13:7384-95. [DOI: 10.1039/c0cp02749a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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MITSUOKA M, SHINZAWA H, MORISAWA Y, KARIYAMA N, HIGASHI N, TSUBOI M, OZAKI Y. Quantitative Analysis of Ions in Spring Water in Three Different Areas of Hyogo Prefecture in Japan by Far Ultraviolet Spectroscopy. ANAL SCI 2011; 27:177-82. [DOI: 10.2116/analsci.27.177] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Ikehata A, Mitsuoka M, Morisawa Y, Kariyama N, Higashi N, Ozaki Y. Effect of Cations on Absorption Bands of First Electronic Transition of Liquid Water. J Phys Chem A 2010; 114:8319-22. [DOI: 10.1021/jp104951m] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Akifumi Ikehata
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
| | - Motoki Mitsuoka
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
| | - Naomi Kariyama
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
| | - Noboru Higashi
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan, National Food Research Institute, National Agriculture and Food Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan, and KURABO Industries Ltd., 14-5 Shimokida-cho, Neyagawa 572-0823, Japan
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QM/MM Approaches to the Electronic Spectra of Hydrogen-Bonding Systems with Connection to Many-Body Decomposition Schemes. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Pathak AK, Mukherjee T, Maity DK. Quantum Chemical Study on UV−vis Spectra of Microhydrated Iodine Dimer Radical Anion. J Phys Chem A 2009; 114:721-4. [DOI: 10.1021/jp9087157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- A. K. Pathak
- Radiation and Photochemistry Division and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - T. Mukherjee
- Radiation and Photochemistry Division and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - D. K. Maity
- Radiation and Photochemistry Division and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai-400085, India
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Galamba N, Mata RA, Cabral BJC. Electronic Excitation of Cl− in Liquid Water and at the Surface of a Cluster: A Sequential Born−Oppenheimer Molecular Dynamics/Quantum Mechanics Approach. J Phys Chem A 2009; 113:14684-90. [DOI: 10.1021/jp904687k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nuno Galamba
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ricardo A. Mata
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Benedito J. Costa Cabral
- Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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Pathak AK, Mukherjee T, Maity DK. Vibrational Analysis of I2•−.nCO2 Clusters (n = 1−10): A First Principle Study on Microsolvation. J Phys Chem A 2008; 112:12037-44. [DOI: 10.1021/jp805348q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- A. K. Pathak
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - T. Mukherjee
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - D. K. Maity
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
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Pathak AK, Mukherjee T, Maity DK. Theoretical Study on the Spectroscopic Properties of CO3.−.nH2O Clusters: Extrapolation to Bulk. Chemphyschem 2008; 9:2259-64. [DOI: 10.1002/cphc.200800429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Electronic Properties and Conformation Analysis of Phytochromobilins, Chromophore in Phytochrome. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.9.1678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Berashevich J, Chakraborty T. Water induced weakly bound electrons in DNA. J Chem Phys 2008; 128:235101. [PMID: 18570530 DOI: 10.1063/1.2939248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have studied the effect of humidity on the electronic properties of DNA base pairs. We found that the hydrogen links of the nucleobases with water molecules lead to a shift of the pi electron density from carbon atoms to nitrogen atoms and can change the symmetry of the wave function for some nucleobases. As a result, the orbital energies are shifted which leads to a decrease in the potential barrier for the hole transfer between the G-C and A-T pairs from 0.7 eV for the dehydrated case to 0.123 eV for the hydrated. More importantly, the pi electron density redistribution activated by hydration is enhanced by the intrastrand interactions. This leads to a modification of the nucleobase chemical structures from the covalent type to a resonance structure with separated charges, where some pi electrons are not locked up into the covalent bonds. Within the (G-C)(2) sequences, there is overlapping of the electronic clouds of such unlocked electrons belonging to the stacked guanines, that significantly increases the electron coupling between them to V(DA)=0.095 eV against the V(DA)=0.025 eV for the dehydrated case. Consequently, the charge transfer between two guanines within the (G-C)(2) sequences is increased by 250 times due to hydration. The presence of nonbonded electrons suppress the band gap up to approximately 3.0 eV, that allows us to consider DNA as a narrow band gap semiconductor.
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Affiliation(s)
- Julia Berashevich
- Department of Physics and Astronomy, The University of Manitoba, Winnipeg R3T 2N2, Canada
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Karthikeyan S, Singh JN, Park M, Kumar R, Kim KS. Structures, energetics, vibrational spectra of NH4+(H2O)n=4,6 clusters: Ab initio calculations and first principles molecular dynamics simulations. J Chem Phys 2008; 128:244304. [DOI: 10.1063/1.2943671] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bochkarev AV. Counterion effects on the isotopic properties of the Cl− and Li+ ions in aqueous solutions. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2008. [DOI: 10.1134/s0036024408050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lee HM, Kolaski M, Kim KS. Photodissociation of Hydrated Hydrogen Iodide Clusters. Chemphyschem 2008; 9:567-71. [DOI: 10.1002/cphc.200700771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Pathak AK, Mukherjee T, Maity DK. Microhydration of NO3-: A Theoretical Study on Structure, Stability and IR Spectra. J Phys Chem A 2008; 112:3399-408. [DOI: 10.1021/jp711108q] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- A. K. Pathak
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - T. Mukherjee
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - D. K. Maity
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
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Kumar A, Kołaski M, Kim KS. Ground state structures and excited state dynamics of pyrrole-water complexes: Ab initio excited state molecular dynamics simulations. J Chem Phys 2008; 128:034304. [DOI: 10.1063/1.2822276] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pathak AK, Mukherjee T, Maity DK. Microhydration of X2 Gas (X = Cl, Br, and I): A Theoretical Study on X2·nH2O Clusters (n = 1−8). J Phys Chem A 2008; 112:744-51. [DOI: 10.1021/jp076594a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- A. K. Pathak
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - T. Mukherjee
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - D. K. Maity
- Radiation and Photochemistry Division, and Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India
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Min SK, Lee EC, Lee HM, Kim DY, Kim D, Kim KS. Complete basis set limit ofAb initio binding energies and geometrical parameters for various typical types of complexes. J Comput Chem 2008; 29:1208-21. [DOI: 10.1002/jcc.20880] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kołaski M, Lee HM, Pak C, Kim KS. Charge-Transfer-to-Solvent-Driven Dissolution Dynamics of I-(H2O)2-5 upon Excitation: Excited-State ab Initio Molecular Dynamics Simulations. J Am Chem Soc 2007; 130:103-12. [DOI: 10.1021/ja072427c] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maciej Kołaski
- Department of Chemistry, Center for Superfunctional Materials, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Han Myoung Lee
- Department of Chemistry, Center for Superfunctional Materials, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Chaeho Pak
- Department of Chemistry, Center for Superfunctional Materials, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
| | - Kwang S. Kim
- Department of Chemistry, Center for Superfunctional Materials, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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Lee HM, Kim D, Singh NJ, Kołaski M, Kim KS. Hydrated hydride anion clusters. J Chem Phys 2007; 127:164311. [DOI: 10.1063/1.2778423] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Singh NJ, Lee EC, Choi YC, Lee HM, Kim KS. Understanding Clusters toward the Design of Functional Molecules and Nanomaterials. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1437] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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50
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SINGH NJITEN, LEE HANMYOUNG, HWANG INCHUL, KIM KWANGS. Designing Ionophores and Molecular Nanotubes Based on Molecular Recognition. Supramol Chem 2007. [DOI: 10.1080/10610270701294480] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- N. JITEN SINGH
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - HAN MYOUNG LEE
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - IN-CHUL HWANG
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - KWANG S. KIM
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
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