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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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Adhikary A, Mohapatra S, Lee SH, Hor YS, Adhikari P, Ching WY, Choudhury A. Metallic Ternary Telluride with Sphalerite Superstructure. Inorg Chem 2016; 55:2114-22. [DOI: 10.1021/acs.inorgchem.5b02516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Puja Adhikari
- Department
of Physics and Astronomy, University of Missouri—Kansas City, Kansas
City, Missouri 64110, United States
| | - Wai-Yim Ching
- Department
of Physics and Astronomy, University of Missouri—Kansas City, Kansas
City, Missouri 64110, United States
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Ivanovskii AL. Boron and its compounds with nonmetals: chemical bonding and the electronic properties. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1997v066n06abeh000280] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Gupta RP, Gupta M. Electronic structure of the non-superconducting compound YBa2Cu3O6. ACTA ACUST UNITED AC 2000. [DOI: 10.1088/0305-4608/18/2/001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Laser Raman evidence for enhanced electron–phonon coupling in a Y–Ba–Cu-oxide superconductor below
T
c
: an application of the maximum entropy method of spectral estimation. ACTA ACUST UNITED AC 1997. [DOI: 10.1098/rspa.1988.0127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This report discusses Raman spectra, recorded at various temperatures from 4.2 to 100 K, of the high-temperature oxidic superconducting material YBa
2
Cu
3
O
7
(
T
c
= 90 K). By utilizing the maximum entropy method (MEM) the Raman bands were separated from the luminescent background. Our results clearly demonstrate significant enhancement of Raman activity, indicative of strong electron–phonon coupling, below the superconducting transition temperature, together with low-temperature ordering of the copper ions in their lattice sites. Several bands may also be attributed to defects of the oxygen lattice, some of which disappear as the reordering occurs.
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Zhao GL, Callaway J, Hayashibara M. Electronic structures of iron and cobalt pyrites. PHYSICAL REVIEW. B, CONDENSED MATTER 1993; 48:15781-15786. [PMID: 10008131 DOI: 10.1103/physrevb.48.15781] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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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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Lu DF, Wong KW, Yeung HY, Fung PC. Mass-anisotropy and oxygen-deficiency effects on the Tc of the YBa2Cu3O7- delta system using the excitonic-enhancement model. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 46:3550-3561. [PMID: 10004073 DOI: 10.1103/physrevb.46.3550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Lu X, Wang SJ, Jean YC, Hor PH, Xue YY, Huang ZJ, Chu CW. Defect properties of neutron-irradiated YBa2Cu3O7 superconductors probed by positron annihilation. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 45:7989-7995. [PMID: 10000607 DOI: 10.1103/physrevb.45.7989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Li D, Xu YN, Ching WY. Electronic structures, total energies, and optical properties of alpha -rhombohedral B12 and alpha -tetragonal B50 crystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1992; 45:5895-5905. [PMID: 10000329 DOI: 10.1103/physrevb.45.5895] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Xu YN, Huang MZ, Ching WY. Optical properties of superconducting K3C60 and insulating K6C60. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 44:13171-13174. [PMID: 9999518 DOI: 10.1103/physrevb.44.13171] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Tsay SF, Wang SY. Plasmon modes in a system composed of Cu-O layers and chains. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:13080-13091. [PMID: 9997130 DOI: 10.1103/physrevb.43.13080] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ching WY, Zhao GL, Xu YN, Wong KW. Orbital-resolved partial density of states in YBa2Cu3O7. PHYSICAL REVIEW. B, CONDENSED MATTER 1991; 43:6159-6162. [PMID: 9998026 DOI: 10.1103/physrevb.43.6159] [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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Bharathi A, Sundar CS, Ching WY, Jean YC, Hor PH, Xue YY, Chu CW. Positron distribution contribution to changes in annihilation characteristics across Tc in high-temperature superconductors. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 42:10199-10210. [PMID: 9995278 DOI: 10.1103/physrevb.42.10199] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ching WY, Xu YN, Harmon BN, Ye J, Leung TC. Electronic structures of FeB, Fe2B, and Fe3B compounds studied using first-principles spin-polarized calculations. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 42:4460-4470. [PMID: 9995976 DOI: 10.1103/physrevb.42.4460] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Zhong XF, Xu YN, Ching WY. Orthogonalized linear combinations of atomic orbitals. IV. Inclusion of relativistic corrections. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:10545-10552. [PMID: 9993463 DOI: 10.1103/physrevb.41.10545] [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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Zhang M, Yin Z, Hu G, Chen Q. Phonon natures in Raman spectra of Y-Ba-Cu-O compounds. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:2003-2008. [PMID: 9993929 DOI: 10.1103/physrevb.41.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Chui ST, Kasowski RV, Hsu WY. First-principles investigation of the superconducting properties of Tl2Ba2CaCu2O8 and the spin instability of Cr using a new approach of configuration-interaction of band-structure wave functions. PHYSICAL REVIEW. B, CONDENSED MATTER 1990; 41:273-281. [PMID: 9992765 DOI: 10.1103/physrevb.41.273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ching WY, Xu YN, Wong KW. Ground-state and optical properties of Cu2O and CuO crystals. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:7684-7695. [PMID: 9991194 DOI: 10.1103/physrevb.40.7684] [Citation(s) in RCA: 101] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Arko AJ, List RS, Bartlett RJ, Cheong S, Fisk Z, Thompson JD, Olson CG, Yang A, Liu R, Gu C, Veal BW, Liu JZ, Paulikas AP, Vandervoort K, Claus H, Campuzano JC, Schirber JE, Shinn ND. Large, dispersive photoelectron Fermi edge and the electronic structure of YBa2Cu3O6.9 single crystals measured at 20 K. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 40:2268-2277. [PMID: 9992108 DOI: 10.1103/physrevb.40.2268] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Costa-Quintana J, López-Aguilar F, Balle S, Salvador R. Electronic structure of YBa2Cu3O7- delta including strong correlation effects. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 39:9675-9678. [PMID: 9947725 DOI: 10.1103/physrevb.39.9675] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Ramsey MG, Netzer FP, Matthew JA. Electron-energy-loss spectra of the high-Tc superconductors Y-Ba-Cu-O and La-Sr-Cu-O. PHYSICAL REVIEW. B, CONDENSED MATTER 1989; 39:732-735. [PMID: 9947214 DOI: 10.1103/physrevb.39.732] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Balseiro CA, Rojo AG, Gagliano ER, Alascio B. Pairing mechanisms in high-Tc superconductors. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:9315-9318. [PMID: 9945743 DOI: 10.1103/physrevb.38.9315] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Song Y, Golben JP, Chittipeddi S, Gaines JR, Epstein AJ. Experimental study of La1Ba2Cu3Ox. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:4605-4615. [PMID: 9946850 DOI: 10.1103/physrevb.38.4605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Press MR, Rao BK, Jena P. Electronic structure of LiBeH3. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:2380-2387. [PMID: 9946541 DOI: 10.1103/physrevb.38.2380] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Chen H, Callaway J, Misra PK. Electronic structure of Cu-O chains in the high-Tc superconductor YBa2Cu3O7. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 38:195-203. [PMID: 9945177 DOI: 10.1103/physrevb.38.195] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Xu Y, Ching WY, Wong KW. Exploratory study of the electronic structure of fluorine-substituted YBa2Cu. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:9773-9776. [PMID: 9944377 DOI: 10.1103/physrevb.37.9773] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Gervais F, Echegut P, Bassat JM, Odier P. Analysis of infrared reflection spectra of oxides of the La2CuO4 high -Tc superconductor family in polarized light. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:9364-9372. [PMID: 9944323 DOI: 10.1103/physrevb.37.9364] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Chen CH, Schneemeyer LF, Liou SH, Hong M, Kwo J, Chen HS, Waszczak JV. Electronic excitations of the YBa2Cu3O7-x superconductor: A study by transmission electron-energy-loss spectroscopy with an electron microprobe. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:9780-9783. [PMID: 9944379 DOI: 10.1103/physrevb.37.9780] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Stoffel NG, Chang Y, Kelly MK, Dottl L, Onellion M, Morris PA, Bonner WA, Margaritondo G. Angle-resolved photoemission studies of single-crystal YBa2Cu. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:7952-7955. [PMID: 9944120 DOI: 10.1103/physrevb.37.7952] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Szpunar B, Smith VH. Linear muffin-tin-orbital atomic-sphere-approximation calculations of the electronic structure of YBa2Cu. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:7525-7528. [PMID: 9944045 DOI: 10.1103/physrevb.37.7525] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Etemad S, Aspnes DE, Kelly MK, Thompson R, Tarascon J, Hull GW. Correlation of dopant-induced optical transitions with superconductivity in La2-xSrxCuO4- delta. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:3396-3399. [PMID: 9944931 DOI: 10.1103/physrevb.37.3396] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Smedskjaer LC, Veal BW, Legnini DG, Paulikas AP, Nowicki LJ. Positron-annihilation studies of the superconductivity transition in YBa2Cu. PHYSICAL REVIEW. B, CONDENSED MATTER 1988; 37:2330-2333. [PMID: 9944767 DOI: 10.1103/physrevb.37.2330] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Chen H, Callaway J, Misra PK. Cluster studies of the electronic structure of Cu-O chains in high-temperature superconductors. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 36:8863-8865. [PMID: 9942731 DOI: 10.1103/physrevb.36.8863] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Ralston JP. Model-independent tests of excitonic enhancement in high-Tc superconductors. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 36:8783-8785. [PMID: 9942706 DOI: 10.1103/physrevb.36.8783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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Zhao GL, Xu Y, Ching WY, Wong KW. Theoretical calculation of optical properties of Y-Ba-Cu-O superconductors. PHYSICAL REVIEW. B, CONDENSED MATTER 1987; 36:7203-7206. [PMID: 9942465 DOI: 10.1103/physrevb.36.7203] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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