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Nanni L. Investigating proton tunneling dynamics in the time-dependent Schrödinger equation. J Comput Chem 2024; 45:1614-1623. [PMID: 38523084 DOI: 10.1002/jcc.27348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 03/26/2024]
Abstract
Understanding the temporal evolution of the wave function in the proton tunneling reactions allows us to make theoretical predictions on the possible femtosecond spectroscopy patterns. However, the analytical solution of the time-dependent Schrödinger equation of complex molecules is challenging and requires a high computational cost. In this study, we solve the time-dependent Schrödinger equation using the Fourier grid Hamiltonian method, highlighting its simplicity of calculation, even for multidimensional tunneling reactions. The obtained model is applied to studying malonaldehyde's two-dimensional intramolecular proton tunneling, comparing the results with those obtained using other computational methods.
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Affiliation(s)
- Luca Nanni
- Department of Physics, University of Ferrara, Ferrara, Italy
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2
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Goli M, Shahbazian S. MC-QTAIM analysis reveals an exotic bond in coherently quantum superposed malonaldehyde. Phys Chem Chem Phys 2023; 25:5718-5730. [PMID: 36744327 DOI: 10.1039/d2cp05499j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The proton between the two oxygen atoms of the malonaldehyde molecule experiences an effective double-well potential in which the proton's wavefunction is delocalized between the two wells. Herein we employ a state-of-the-art multi-component quantum theory of atoms in molecules partitioning scheme to obtain the molecular structure, i.e. atoms in molecules and bonding network, from the superposed ab initio wavefunctions of malonaldehyde. In contrast to the familiar clamped-proton portrayal of malonaldehyde, in which the proton forms a hydrogen basin, for the superposed states the hydrogen basin disappears and two novel hybrid oxygen-hydrogen basins appear instead, with an even distribution of the proton population between the two basins. The interaction between the hybrid basins is stabilizing thanks to an unprecedented mechanism. This involves the stabilizing classical Coulomb interaction of the one-proton density in one of the basins with one-electron density in the other basin. This stabilizing mechanism yields a bond foreign to the known bonding modes in chemistry.
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Affiliation(s)
- Mohammad Goli
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran.
| | - Shant Shahbazian
- Department of Physics, Shahid Beheshti University, Evin, Tehran, Iran.
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3
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Gutiérrez-Quintanilla A, Chevalier M, Platakyte R, Ceponkus J, Crépin C. Selective photoisomerisation of 2-chloromalonaldehyde. J Chem Phys 2019; 150:034305. [PMID: 30660154 DOI: 10.1063/1.5082916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Isomerization of 2-chloromalonaldehyde (2-ClMA) is explored giving access to new experimental data on this derivative of malonaldehyde, not yet studied much. Experiments were performed isolating 2-ClMA in argon, neon, and para-hydrogen matrices. UV irradiation of the matrix samples induced isomerization to three open enolic forms including two previously observed along with the closed enolic form after deposition. IR spectra of these specific conformers were recorded, and a clear assignment of the observed bands was obtained with the assistance of theoretical calculations. UV spectra of the samples were measured, showing a blue shift of the π* ← π absorption with the opening of the internal hydrogen bond of the most stable enol form. Specific sequences of UV irradiation at different wavelengths allowed us to obtain samples containing only one enol conformer. The formation of conformers is discussed. The observed selectivity of the process among the enol forms is analyzed.
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Affiliation(s)
- Alejandro Gutiérrez-Quintanilla
- Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, CNRS, Université Paris- Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Michèle Chevalier
- Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, CNRS, Université Paris- Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Rasa Platakyte
- Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, CNRS, Université Paris- Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Justinas Ceponkus
- Institute of Chemical Physics, Vilnius University, Sauletekio ave. 9 bat. III, L-10222 Vilnius, Lithuania
| | - Claudine Crépin
- Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, CNRS, Université Paris- Sud, Université Paris-Saclay, F-91405 Orsay, France
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4
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Yang Y, Li D, Li C, Liu Y, Jiang K. Asymmetric substitution changes the UV-induced nonradiative decay pathway and the spectra behaviors of β-diketones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 207:209-215. [PMID: 30240982 DOI: 10.1016/j.saa.2018.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Asymmetric substitution has not been termed as an essential factor in studying photo-induced ultrafast dynamics of molecular system. Asymmetric 4-hydroxybut-3-en-2-one (HEO), together with symmetric malonaldehyde (MA) and acetylacetone (AA), have been provided as target sample to study the nonradiative decay (ND) processes of β-diketones. An effective ND pathway of the three molecules is presented that their excited second (S2) states transfer to first (S1) state by nonadiabatic surface hopping, and then transfer to triplet (T1) state by crossing minimum energy crossing point (MECP), after which decay to ground (S0) state through MECP. More importantly, the asymmetric substitution of HEO induces the proton transfer in the S1 state and generates a proton-transferred conformer with lowest energy, which does not occur for MA and AA. This change exploits a new ND pathway that the S1 state decays to the proton transferred T1 state and then undergoes reverse proton transfer to S0 state through the MECPs between the three states. The two pathways of HEO give detailed energy and geometric information on surface hopping of S2/S1 and MECPs of S1/T1/S0, and interpret the reason of the ND pathway while not spectra emission. This result is significantly different from the previous reported ND pathway of photoisomerization or conical intersection between different states. This work shows that asymmetric substitution changes the molecular structure and then changes their spectra behaviors.
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Affiliation(s)
- Yonggang Yang
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Donglin Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Chaozheng Li
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China
| | - Yufang Liu
- College of Physics and Materials Science, Henan Normal University, Xinxiang 453007, China.
| | - Kai Jiang
- School of Environment, Henan Normal University, Xinxiang 453007, China
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5
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Durlak P, Latajka Z. Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car‐parrinello and path integral molecular dynamics. J Comput Chem 2018; 40:671-687. [DOI: 10.1002/jcc.25753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/21/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Durlak
- Faculty of ChemistryUniversity of Wrocław Wrocław 50‐383 Poland
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6
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Durlak P, Latajka Z. Car–Parrinello and Path Integral Molecular Dynamics Study of the Proton Transfer in the Intramolecular Hydrogen Bonds in the Ketohydrazone–Azoenol System. J Phys Chem B 2018; 122:7862-7873. [DOI: 10.1021/acs.jpcb.8b04883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Durlak
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Zdzisław Latajka
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
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7
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Massarczyk M, Schlitter J, Kötting C, Rudack T, Gerwert K. Monitoring transient events in infrared spectra using local mode analysis. Proteins 2018; 86:1013-1019. [PMID: 30019772 DOI: 10.1002/prot.25536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 01/10/2023]
Abstract
Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.
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Affiliation(s)
| | - Jürgen Schlitter
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
| | - Klaus Gerwert
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
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8
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Gutiérrez-Quintanilla A, Chevalier M, Platakyte R, Ceponkus J, Rojas-Lorenzo GA, Crépin C. 2-Chloromalonaldehyde, a model system of resonance-assisted hydrogen bonding: vibrational investigation. Phys Chem Chem Phys 2018; 20:12888-12897. [PMID: 29700529 DOI: 10.1039/c7cp06481k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The chelated enol isomer of 2-chloromalonaldehyde (2-ClMA) is experimentally characterized for the first time by IR and Raman spectroscopies. The spectra are obtained by trapping the molecule in cryogenic matrices and analyzed with the assistance of theoretical calculations. Experiments were performed in argon, neon and para-hydrogen matrices. The results highlight puzzling matrix effects, beyond site effects, which are interpreted as due to a tunneling splitting of the vibrational levels related to the proton transfer along the internal hydrogen bond (IHB). 2-ClMA is thus one of the very few molecules in which the H tunneling has been observed in cryogenic matrices. The comparison with its parent molecule (malonaldehyde) shows experimentally and theoretically the weakening of the IHB upon chlorination, with a reduced cooperative effect in the resonance assisted hydrogen bond. In addition, the Cl substitution induces an important stabilization of two open enol conformers. These two open forms appear in the spectra of as-deposited samples, meaning that, in contrast with other well-studied molecules of the same family (β-dialdehydes and β-diketones), they are present in the gas phase at room temperature.
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Affiliation(s)
- Alejandro Gutiérrez-Quintanilla
- Institut des Sciences Moléculaires d'Orsay (ISMO), UMR 8214, CNRS, Univ. Paris-Sud, Université Paris-Saclay UMR 8214, F-91405 Orsay, France
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Goli M, Shahbazian S. Muon-Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution. Chemistry 2016; 22:2525-31. [PMID: 26749489 DOI: 10.1002/chem.201504318] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Indexed: 12/25/2022]
Abstract
Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014, 53, 13706-13709; Angew. Chem. 2014, 126, 13925-13929] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear-electronic orbital non-Born-Oppenheimer procedure, the nuclear configuration of the muon-substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structure of the muon-substituted malonaldehyde and the AIM structure of the stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehyde to the transition state.
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Affiliation(s)
- Mohammad Goli
- Faculty of Chemistry, Shahid Beheshti University, G. C., Evin, P.O. Box 19395-4716, Tehran, 19839, Iran), Fax
| | - Shant Shahbazian
- Faculty of Chemistry, Shahid Beheshti University, G. C., Evin, P.O. Box 19395-4716, Tehran, 19839, Iran), Fax.
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Kubař T, Welke K, Groenhof G. New QM/MM implementation of the DFTB3 method in the gromacs package. J Comput Chem 2015; 36:1978-89. [PMID: 26238364 DOI: 10.1002/jcc.24029] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/09/2015] [Indexed: 01/07/2023]
Abstract
The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle-mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron-induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization.
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Affiliation(s)
- Tomáš Kubař
- Institute of Physical Chemistry and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, 76131, Germany
| | - Kai Welke
- Department of Chemistry, Nagoya University, Nagoya, 464-8602, Japan
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Jyväskylä, 40014, Finland
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11
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Jalali E, Nori-Shargh D. Symmetry breaking in the axial symmetrical configurations of enolic propanedial, propanedithial, and propanediselenal: pseudo Jahn–Teller effect versus the resonance-assisted hydrogen bond theory. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The origin of the symmetry breaking in the axial symmetrical configurations of enolic propanedial (1), propanedithial (2), and propanediselenal (3) have been investigated by means of time-dependence density functional theory and natural bond orbital interpretations. The results obtained at the quantum chemistry composite (G2MP2, CBS-QB3), ab initio molecular orbital (MP2/6-311++G**), and hybrid density functional theory (B3LYP/6-311++G**) levels of theory showed that the hydrogen-centered synchronous axial symmetrical (C2v) configurations of compounds 1–3 possessing the maximum π-electron delocalization within the M1=C2–C3=C4–M5–H6 keto-enol groups are less stable than their corresponding plane symmetrical (Cs) forms. Importantly, the symmetry breaking in the C2v configurations of the enol forms of compounds 1–3 to their corresponding plane symmetrical Cs configurations is due to the pseudo Jahn–Teller effect (PJTE) by mixing the ground A1 and excited B2 electronic states resulting in a PJT (A1 + B2) ⊗ b2 problem. We may expect that by the decrease of the energy gaps between reference states in the C2v forms that are involved in the PJTE decrease from compound 1 to compound 3, the PJT stabilization energy (PJTSE) may increase but the results obtained showed that the corresponding PJTSEs decrease. This fact can be justified by the increase of the electron delocalizations from the nonbonding orbitals of the C=M moieties to the antibonding orbitals of the H–M bonds, which leads to an increase of the π-electron delocalization within the M1=C2–C3=C4–M5–H6 keto-enol groups. In confrontation between the impacts of the resonance-assisted hydrogen bond and PJTE in the structural and configurational properties of compounds 1–3, PJTE has an overwhelming contribution and causes the symmetry breaking of the C2v configurations to their corresponding Cs forms. The correlations between the structural parameters, synchronicity indices, natural charges, PJTSEs, electron delocalizations, and the hardness of compounds 1–3 have been investigated.
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Affiliation(s)
- Elahe Jalali
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
| | - Davood Nori-Shargh
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
- Department of Chemistry, Arak Branch, Islamic Azad University, Arak, Iran
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13
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Durlak P, Mierzwicki K, Latajka Z. Investigations of the Very Short Hydrogen Bond in the Crystal of Nitromalonamide via Car–Parrinello and Path Integral Molecular Dynamics. J Phys Chem B 2013; 117:5430-40. [DOI: 10.1021/jp312473b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Durlak
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Krzysztof Mierzwicki
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
| | - Zdzisław Latajka
- Faculty
of Chemistry, University of Wrocław,
14 F. Joliot-Curie Street, 50-383 Wrocław, Poland
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14
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The two-component quantum theory of atoms in molecules (TC-QTAIM): tensor formulation and its implications. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1362-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Fillaux F, Cousson A. Neutron scattering studies of K3H(SO4)2 and K3D(SO4)2: The particle-in-a-box model for the quantum phase transition. J Chem Phys 2012; 137:074504. [DOI: 10.1063/1.4745181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Mazziotti DA. Two-Electron Reduced Density Matrix as the Basic Variable in Many-Electron Quantum Chemistry and Physics. Chem Rev 2011; 112:244-62. [DOI: 10.1021/cr2000493] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David A. Mazziotti
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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McKee ML. Fluctional molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.47] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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