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Adhikari P, Podgornik R, Jawad B, Ching WY. First-Principles Simulation of Dielectric Function in Biomolecules. MATERIALS (BASEL, SWITZERLAND) 2021; 14:5774. [PMID: 34640170 PMCID: PMC8510404 DOI: 10.3390/ma14195774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023]
Abstract
The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2-5.7 eV and 14.4-15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.
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Affiliation(s)
- Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
| | - Rudolf Podgornik
- School of Physical Sciences, Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (P.A.); (B.J.)
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Yoshikawa G, Tsuruma Y, Ikeda S, Saiki K. Noble metal intercalated fullerene fabricated by low-temperature co-deposition. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:43-46. [PMID: 20217694 DOI: 10.1002/adma.200900921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Genki Yoshikawa
- World Premier International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba, Ibaraki, Japan.
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Roman H, Colò G, Alasia F, Broglia R. Long wavelength optical response of incipient fullerene nanotubes. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(96)00064-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Xu YN, Ching WY, Jean YC, Lou Y. First-principles calculation of the electronic and optical properties of the organic superconductor kappa -(BEDT-TTF)2Cu(NCS)2. PHYSICAL REVIEW. B, CONDENSED MATTER 1995; 52:12946-12950. [PMID: 9980466 DOI: 10.1103/physrevb.52.12946] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Xu YN, Ching WY. Electronic bonding and optical properties of the H2-H2O phase at high pressure. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 50:17709-17712. [PMID: 9976197 DOI: 10.1103/physrevb.50.17709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Degiorgi L, Nicol EJ, Klein O, Grüner G, Wachter P, Huang S, Wiley J, Kaner RB. Optical properties of the alkali-metal-doped superconducting fullerenes: K3C60 and Rb3C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:7012-7025. [PMID: 10009429 DOI: 10.1103/physrevb.49.7012] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Yu J, Bi L, Kalia RK, Vashishta P. Intermolecular and intramolecular phonons in solid C60: Effects of orientational disorder and pressure. PHYSICAL REVIEW. B, CONDENSED MATTER 1994; 49:5008-5019. [PMID: 10011436 DOI: 10.1103/physrevb.49.5008] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Yu J, Kalia RK, Vashishta P. Effect of pressure on intermolecular and intramolecular phonons in solid C60. J Chem Phys 1993. [DOI: 10.1063/1.465504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Brühwiler PA, Maxwell AJ, Nilsson A, Mårtensson N, Gunnarsson O. Auger and photoelectron study of the Hubbard U in C60, K3C60, and K6C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:18296-18299. [PMID: 10008479 DOI: 10.1103/physrevb.48.18296] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Stafström S, Brédas JL, Lögdlund M, Salaneck WR. Charge storage states in polyenes. J Chem Phys 1993. [DOI: 10.1063/1.465672] [Citation(s) in RCA: 19] [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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Resca L. Comment on "First-principles calculation of optical properties of C60 in the fcc lattice". PHYSICAL REVIEW LETTERS 1993; 71:2839. [PMID: 10054790 DOI: 10.1103/physrevlett.71.2839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Evangelisti F. Electronic states at the Fermi level of doped C60. PHYSICAL REVIEW LETTERS 1993; 71:2477-2480. [PMID: 10054690 DOI: 10.1103/physrevlett.71.2477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Xu YN, Ching WY. Electronic, optical, and structural properties of some wurtzite crystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:4335-4351. [PMID: 10008905 DOI: 10.1103/physrevb.48.4335] [Citation(s) in RCA: 275] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Wilson WL, Hebard AF, Narasimhan LR, Haddon RC. Doping-induced spectral evolution in C60: Evidence of immiscible stoichiometric phases in AxC60 (A=K,Rb; x=0, 3, and 6) thin films. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:2738-2742. [PMID: 10008673 DOI: 10.1103/physrevb.48.2738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Saito S, Oshiyama A. Sr6C60 and Ba6C60: Semimetallic fullerides. PHYSICAL REVIEW LETTERS 1993; 71:121-124. [PMID: 10054388 DOI: 10.1103/physrevlett.71.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Sohmen E, Fink J. Electron-energy-loss studies of RbxC60 and RbxC70 (x=0, 3, and 6). PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:14532-14540. [PMID: 10005808 DOI: 10.1103/physrevb.47.14532] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Benning PJ, Stepniak F, Poirier DM, Martins JL, Weaver JH, Chibante LP, Smalley RE. Electronic properties of K-doped C60(111): Photoemission and electron correlation. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:13843-13847. [PMID: 10005705 DOI: 10.1103/physrevb.47.13843] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Huang MZ, Xu YN, Ching WY. Pressure dependence of the band structure, density of states, Fermi surfaces, and optical properties of superconducting K3C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:8249-8259. [PMID: 10004837 DOI: 10.1103/physrevb.47.8249] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Huang MZ, Ching WY, Lenosky T. Electronic properties of negative-curvature periodic graphitic carbon surfaces. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 47:1593-1606. [PMID: 10006176 DOI: 10.1103/physrevb.47.1593] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Huant S, Robert JB, Chouteau G, Bernier P, Fabre C, Rassat A. Lattice phonon modes in solid C60 studied by far-infrared spectroscopy. PHYSICAL REVIEW LETTERS 1992; 69:2666-2669. [PMID: 10046553 DOI: 10.1103/physrevlett.69.2666] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Degiorgi L, Grüner G, Wachter P, Huang S, Wiley J, Whetten RL, Kaner RB, Holczer K, Diederich F. Electrodynamic response of Rb3C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:11250-11253. [PMID: 10003012 DOI: 10.1103/physrevb.46.11250] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ching WY, Huang MZ, Xu Y. Electronic and optical properties of the Vanderbilt-Tersoff model of negative-curvature fullerene. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:9910-9912. [PMID: 10002827 DOI: 10.1103/physrevb.46.9910] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Huang MZ, Xu YN, Ching WY. Electronic structures of K3C60, RbK2C60, Rb2KC60, Rb3C60, Rb2CsC60, and Cs3C60 crystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:6572-6577. [PMID: 10002346 DOI: 10.1103/physrevb.46.6572] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Lou Y, Lu X, Dai GH, Ching WY, Xu Y, Huang M, Tseng PK, Jean YC, Meng RL, Hor PH, Chu CW. High sensitivity of the positron-density distribution to the K doping in C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:2644-2647. [PMID: 10003950 DOI: 10.1103/physrevb.46.2644] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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