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Mikkelsen JES, Jensen F. Ambiguities in Decomposing Molecular Polarizability into Atomic Charge Flow and Induced Dipole Contributions. J Phys Chem A 2024; 128:4168-4175. [PMID: 38743593 DOI: 10.1021/acs.jpca.4c01890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The molecular dipole polarizability can be decomposed into components corresponding to the charge flow between atoms and changes in atomic dipole moments. Such decompositions are recognized to depend on how atoms are defined within a molecule, as, for example, by Hirshfeld, iterative Stockholder, or quantum topology partitioning of the electron density. For some of these, however, there are significant differences between the numerical results obtained by analytical response methods and finite field calculations. We show that this difference is due to analytical response methods accounting for (only) the change in electron density by a perturbation, while finite field methods may also include a component corresponding to a perturbation-dependent change in the definition of an atom within a molecule. For some atom-in-molecule definitions, such as the iterative Hirshfeld, iterative Stockholder, and quantum topology methods, the latter effect significantly increases the charge flow component. The decomposition of molecular polarizability into atomic charge flow and induced dipole components thus depends on whether the atom-in-molecule definition is taken to be perturbation-dependent.
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Affiliation(s)
- Jonas E S Mikkelsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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Zhou H, Ren Z, Li D, Xu C, Mu X, Lee C. Dynamic construction of refractive index-dependent vibrations using surface plasmon-phonon polaritons. Nat Commun 2023; 14:7316. [PMID: 37952033 PMCID: PMC10640644 DOI: 10.1038/s41467-023-43127-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/01/2023] [Indexed: 11/14/2023] Open
Abstract
One of the fundamental hurdles in infrared spectroscopy is the failure of molecular identification when their infrared vibrational fingerprints overlap. Refractive index (RI) is another intrinsic property of molecules associated with electronic polarizability, but with limited contribution to molecular identification in mixed environments currently. Here, we investigate the coupling mode of localized surface plasmon and surface phonon polaritons for vibrational de-overlapping. The coupling mode is sensitive to the molecular refractive index, attributed to the RI-induced vibrational variations of surface phonon polaritons (SPhP) within the Reststrahlen band, referred to as RI-dependent SPhP vibrations. The RI-dependent SPhP vibrations are linked to molecular RI features. According to the deep-learning-augmented demonstration of bond-breaking-bond-making dynamic profiling in biological reaction, we substantiate that the RI-dependent SPhP vibrations effectively disentangle overlapping vibrational modes, achieving a 92% identification accuracy even for the strongly overlapping vibrational modes in the reaction. Our findings offer insights into the realm of light-matter interaction and provide a valuable toolkit for biomedicine applications.
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Affiliation(s)
- Hong Zhou
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117583, Singapore
| | - Zhihao Ren
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117583, Singapore
| | - Dongxiao Li
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117583, Singapore
| | - Cheng Xu
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117583, Singapore
| | - Xiaojing Mu
- Key Laboratory of Optoelectronic Technology & Systems of Ministry of Education, International R&D Center of Micro-Nano Systems and New Materials Technology, Chongqing University, Chongqing, 400044, P. R. China.
| | - Chengkuo Lee
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, 117583, Singapore.
- Center for Intelligent Sensors and MEMS (CISM), National University of Singapore, Singapore, 117583, Singapore.
- NUS Suzhou Research Institute (NUSRI), Suzhou, Jiangsu, 215123, China.
- NUS Graduate School-Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, 119077, Singapore.
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Jensen F. Unifying Charge-Flow Polarization Models. J Chem Theory Comput 2023. [PMID: 37365806 DOI: 10.1021/acs.jctc.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
We show that several models where electric polarization in molecular systems is modeled by charge-flow between atoms can all be considered as different manifestations of a general underlying mathematical structure. The models can be classified according to whether they employ atomic or bond parameters and whether they employ atom/bond hardness or softness. We show that an ab initio calculated charge response kernel can be considered as the inverse screened Coulombic matrix projected onto the zero-charge subspace, and this may provide a method for deriving charge screening functions to be used in force fields. The analysis suggests that some models contain redundancies, and we argue that a parameterization of charge-flow models in terms of bond softness is preferable as it depends on local quantities and decay to zero upon bond dissociation, while bond hardness depends on global quantities and increases toward infinity upon bond dissociation.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, Aarhus DK-8000, Denmark
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Abstract
We review different models for introducing electric polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been included in several force fields, the common approach has been to focus on atomic dipole polarizability. Several approaches allow modelling electric polarization by using charge-flow between charge sites instead, but this has been less exploited, despite that atomic charges and charge-flow is expected to be more important than atomic dipoles and dipole polarizability. A number of challenges are required to be solved for charge-flow models to be incorporated into polarizable force fields, for example how to parameterize the models and how to make them computational efficient.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Denmark.
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Gao XC, Hao Q, Wang CS. Improved Polarizable Dipole–Dipole Interaction Model for Hydrogen Bonding, Stacking, T-Shaped, and X–H···π Interactions. J Chem Theory Comput 2017; 13:2730-2741. [DOI: 10.1021/acs.jctc.6b00936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xi-Chan Gao
- School of Chemistry and Chemical
Engineering, Liaoning Normal University, Dalian 116029, P. R. China
| | - Qiang Hao
- School of Chemistry and Chemical
Engineering, Liaoning Normal University, Dalian 116029, P. R. China
| | - Chang-Sheng Wang
- School of Chemistry and Chemical
Engineering, Liaoning Normal University, Dalian 116029, P. R. China
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Spectroscopic and time domain reflectometry studies on acetonitrile - Ethylene glycol binary solutions. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Stoppa A, Nazet A, Buchner R, Thoman A, Walther M. Dielectric response and collective dynamics of acetonitrile. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.03.045] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Palombo F, Sassi P, Paolantoni M, Barontini C, Morresi A, Giorgini MG. Complex Dynamical Aspects of Organic Electrolyte Solutions. J Phys Chem B 2013; 118:215-25. [DOI: 10.1021/jp4066604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Francesca Palombo
- School of Physics, University of Exeter , EX4 4QF Exeter, United Kingdom
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Nakano H, Yamamoto T. Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent. J Chem Phys 2012; 136:134107. [DOI: 10.1063/1.3699234] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Palombo F, Paolantoni M, Sassi P, Morresi A, Giorgini MG. Molecular dynamics of liquid acetone determined by depolarized Rayleigh and low-frequency Raman scattering spectroscopy. Phys Chem Chem Phys 2011; 13:16197-207. [DOI: 10.1039/c1cp21806a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Nakano H, Yamamoto T, Kato S. A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids. J Chem Phys 2010; 132:044106. [PMID: 20113018 DOI: 10.1063/1.3298873] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We first describe a wave-function based formalism of polarizable charge model by starting from the Hartree product ansatz for the total wave function and making the second-order expansion of individual molecular energies with the use of partial charge operators. The resulting model is shown to be formally equivalent to the charge response kernel model that starts from the linear-response approximation to partial charges, and also closely related to a family of fluctuating charge models that are based on the electronegativity equalization principle. We then apply the above model to a systematic comparison of polarization effects on qualitatively different liquids, namely, protic solvents (water and methanol), an aprotic polar solvent (acetonitrile), and imidazolium-based ionic liquids. Electronic polarization is known to decelerate molecular motions in conventional solvents while it accelerates them in ionic liquids. To obtain more insights into these phenomena, we consider an effective decomposition of total polarization energy into molecular contributions, and show that their statistical distribution is well-correlated with the acceleration/deceleration of molecular motions. In addition, we perform effective nonpolarizable simulations based on mean polarized charges, and compare them with fully polarizable simulations. The result shows that the former can reproduce structural properties of conventional solvents rather accurately, while they fail qualitatively to reproduce acceleration of molecular motions in ionic liquids.
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Affiliation(s)
- Hiroshi Nakano
- Department of Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Isegawa M, Kato S. Polarizable Force Field for Protein with Charge Response Kernel. J Chem Theory Comput 2009; 5:2809-21. [PMID: 26631793 DOI: 10.1021/ct900295u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We present a molecular mechanical force field for polypeptides and proteins involving the electronic polarization effect described with the charge response kernel. All of the electrostatic parameters for 20 amino acids are obtained by ab initio electronic structure calculations and combined with the AMBER99 force field. The refittings of dihedral angle parameters in the torsional potentials are performed so as to reproduce the ab initio optimized geometries and relative energies for the conformers of dipeptides. The present force field is applied to molecular dynamics simulation calculations of the extended alanine tetra and cyclic pentapeptides in aqueous solution. The infrared spectra are calculated in order to analyze the charge polarization effect on the spectral profiles.
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Affiliation(s)
- Miho Isegawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Kato
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
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Hunger J, Stoppa A, Thoman A, Walther M, Buchner R. Broadband dielectric response of dichloromethane. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.02.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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