Engineering topics

Ching, Wai-Yim

Publications and source records attributed to Ching, Wai-Yim.

At least 19 records

DOE OSTI2023

Porosity modeling in a TiNbTaZrMo high-entropy alloy for biomedical applications

High-entropy alloys (HEAs) have attracted great attention for many biomedical applications. However, the nature of interatomic interactions in this class of complex multicomponent alloys is not fully understood. We report, for the first time, the results of theoretical modeling for porosity in a large biocompatible HEA TiNbTaZrMo using an atomistic supercell of 1024 atoms that provides new insights and understanding. Our results demonstrated the deficiency of using the valence electron count, quantification of large lattice distortion, validation of mechanical properties with available experimental data to reduce Young's modulus. We utilized the novel concepts of the total bond order density (TBOD) and partial bond order density (PBOD) via ab initio quantum mechanical calculations as an effective theoretical means to chart a road map for the rational design of complex multicomponent HEAs for biomedical applications.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Ab initio study of mechanical and thermal properties of GeTe-based and PbSe-based high-entropy chalcogenides

GeTe-based and PbSe-based high-entropy compounds have outstanding thermoelectric (TE) performance and crucial applications in mid and high temperatures. Recently, the optimization of TE performance of high-entropy compounds has been focused on reducing thermal conductivity by strengthening the phonon scattering process to improve TE performance. We report a first-principles investigation on nine GeTe-based high-entropy chalcogenide solid solutions constituted of eight metallic elements (Ag, Pb, Sb, Bi, Cu, Cd, Mn, and Sn) and 13 PbSe-based high-entropy chalcogenide solid solutions: Pb 0.99-y Sb 0.012 Sn y Se 1-2x Te x S x (x = 0.1, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, and y = 0) and Pb 0.99-y Sb 0.012 Sn y Se 1-2x Te x S x (y = 0.05, 0.1, 0.15, 0.2, 0.25 and x = 0.25). We have investigated the mechanical properties focusing on Debye temperature (Θ D ), thermal conductivity (κ), Grüneisen parameter (γ α ), dominant phonon wavelength (λ dom ), and melting temperature (T m ). We find that the lattice thermal conductivity is significantly reduced when GeTe is alloyed into the following compositions: Ge 0.75 Sb 0.13 Pb 0.12 Te, Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te, and Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Mn 0.05 Bi 0.01 Te. This reduction is due to the mass increase and strain fluctuations. The results also show that Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te solid solution has the lowest Young’s modulus (30.362 GPa), bulk and shear moduli (18.626 and 12.359 GPa), average sound velocity (1653.128 m/sec), Debye temperature (151.689 K), lattice thermal conductivity (0.574 W.m –1 .K –1 ), dominant phonon wavelength (0.692 Å), and melting temperature (535.91 K). Moreover, Ge 0.61 Ag 0.11 Sb 0.13 Pb 0.12 Bi 0.01 Te has the highest Grüneisen parameter with a reduced and temperature-independent lattice thermal conductivity. The positive correlation between Θ D and κ is revealed. Alloying of PbSe-based high-entropy by Sb, Sn, Te, and S atoms at the Se and Pb sites resulted in much higher shear strains resulted in the reduction of phonon velocity, a reduced Θ D , and a lower lattice thermal conductivity.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Electronic Structure and Mechanical Properties of Solvated Montmorillonite Clay Using Large-Scale DFT Method

Montmorillonite clay (MMT) has been widely used in engineering and environmental applications as a landfill barrier and toxic waste repository due to its unique property as an expandable clay mineral that can absorb water easily. This absorption process rendered MMT to be highly exothermic due to electrostatic interactions among molecules and hydrogen bonds between surface atoms. A detailed study of a large supercell model of structural clay enables us to predict long-term nuclear waste storage. Herein, a large solvent MMT model with 4071 atoms is studied using ab initio density functional theory. The DFT calculation and analysis clarify the important issues, such as bond strength, solvation effect, elasticity, and seismic wave velocities. These results are compared to our previous study on crystalline MMT (dry). The solvated MMT has reduced shear modulus (G), bulk modulus (K), and Young’s modulus (E). We observe that the conduction band (CB) in the density of states (DOS) of solvated MMT model has a single, conspicuous peak at –8.5 eV. Moreover, the atom-resolved partial density of states (PDOS) summarizes the roles played by each atom in the DOS. These findings illuminate numerous potential sophisticated applications of MMT clay.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid–amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Ab Initio Simulation of Structure and Properties in Ni-Based Superalloys: Haynes282 and Inconel740

The electronic structure, interatomic bonding, and mechanical properties of two supercell models of Ni-based superalloys are calculated using ab initio density functional theory methods. The alloys, Haynes282 and Inconel740, are face-centered cubic lattices with 864 atoms and eleven elements. These multi-component alloys have very complex electronic structure, bonding and partial-charge distributions depending on the composition and strength of the local bonding environment. We employ the novel concept of total bond order density (TBOD) and its partial components (PBOD) to ascertain the internal cohesion that controls the intricate balance between the propensity of metallic bonding between Ni, Cr and Co, and the strong bonds with C and Al. We find Inconel740 has slightly stronger mechanical properties than Haynes282. Both Inconel740 and Haynes282 show ductile natures based on Poisson’s ratio. Poisson’s ratio shows marginal correlation with the TBOD. Comparison with more conventional high entropy alloys with equal components are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein

The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2' cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

First-Principles Calculations of the Structural, Electronic, Optical, and Mechanical Properties of 21 Pyrophosphate Crystals

Pyrophosphate crystals have a wide array of applications in industrial and biomedical fields. However, fundamental understanding of their electronic structure, optical, and mechanical properties is still scattered and incomplete. In the present research, we report a comprehensive theoretical investigation of 21 pyrophosphates A 2 M (H 2 P 2 O 7 ) 2 •2H 2 O with either triclinic or orthorhombic crystal structure. The molecule H 2 P 2 O 7 is the dominant molecular unit, whereas A = (K, Rb, NH 4 , Tl), M = (Zn, Cu, Mg, Ni, Co, Mn), and H 2 O stand for the cation elements, transition metals, and the water molecules, respectively. The electronic structure, interatomic bonding, partial charge distribution, optical properties, and mechanical properties are investigated by first-principles calculations based on density functional theory (DFT). Most of these 21 crystals are theoretically investigated for the first time. The calculated results show a complex interplay between A, M, H 2 P 2 O 7 , and H 2 O, resulting in either metallic, half-metallic, or semi-conducting characteristics. The novel concept of total bond order density (TBOD) is used as a single quantum mechanical metric to characterize the internal cohesion of these crystals to correlate with the calculated properties, especially the mechanical properties. This work provides a large database for pyrophosphate crystals and a road map for potential applications of a wider variety of phosphates.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Role of chemical disorder on radiation-induced defect production and damage evolution in NiFeCoCr

Understanding chemical disorder in many concentrated solid solution alloys (CSAs) at the levels of electrons and atoms has attracted increasing attention as a path forward to reveal and identify underlying mechanisms for extraordinary mechanical properties and improved radiation tolerance. Single-phase NiFeCoCr CSA is a common base for many high-entropy alloys (HEAs) that have shown improved mechanical strength and radiation tolerance. In this study, defect production and damage evolution in NiFeCoCr under ion irradiation at room temperature to dose over 20 dpa are determined using ion channeling technique along both <100> and <110> directions utilizing multiple probing beam energies. The results obtained from the multi-axial and multi-energy channeling analysis are compared with those previously obtained for Ni crystals irradiated under similar conditions. The influence of chemical complexity on defect production and clustering at early-stage under room temperature irradiation up to dose of 1 dpa is discussed based on positron annihilation spectroscopy results. Defect structure evaluation in Ni and NiFeCoCr is also discussed based on transmission electron microscopy results over a prolonged irradiation at both room and elevated temperatures. Compared with chemically complex NiFeCoCr, larger dislocation loops thus less lattice strain are expected to form in pure Ni. Moreover, the role of chemical disorder in this CSA is also investigated based on ab initio calculations using large supercells. Finally, to understand the impact of chemical complexity effect on defect structure evolution, this integrated research effort attempts to link the relatively large charge redistribution due to difference in valence electron counts resulting from alloying different 3d transition metal elements, moderate lattice distortion arising from similar adaptable atomic size, and notable suppressed or delayed damage evolution in NiFeCoCr.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Multi-modal Approach to Modeling Creep Deformation in Nickel-base Superalloy

This study developed the multi-modal modeling approaches to elucidate the physical and overall mechanical properties of two complex alloy systems of Ni-based Superalloys, namely Haynes 282 and Inconel 740. The overall strategies employed systematically in different scales of modeling are based on the common structural framework of the multi phases that made up the Ni-based Superalloys, namely the matrix phase of the Gamma ($\gamma$) phase which is embedded with ordered Gamma prime ($\gamma$’) precipitates and decorated with the dispersions of mostly carbide precipitates. With this in mind, we had set up the modeling platforms to incorporate a wide range of scales, starting from electronic structures to the continuum level via the crystal plasticity model.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2022

Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant

The emergence of new SARS-CoV-2 Omicron variant of concern (OV) has exacerbated the COVID-19 pandemic because of a large number of mutations in the spike protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strains. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly predominantly because of strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

First-Principles Calculations of Thermoelectric Transport Properties of Quaternary and Ternary Bulk Chalcogenide Crystals

Chalcogenide crystals have a wide range of applications, especially as thermoelectric materials for energy conversion. Thermoelectric materials can be used to generate an electric current from a temperature gradient based on the Seebeck effect and based on the Peltier effect, and they can be used in cooling applications. Using first-principles calculations and semiclassical Boltzmann theory, we have computed the Seebeck coefficient, electrical conductivity, electronic thermal conductivity, power factor, and figure of merit of 30 chalcogenide crystals. A Quantum Espresso package is used to calculate the electronic properties and locate the Fermi level. The transport properties are then calculated using the BoltzTraP code. The 30 crystals are divided into two groups. The first group has four crystals with quaternary composition (A 2 BCQ 4 ) (A = Tl; B = Cd, Hg; C = Si, Ge, Sn; Q = S, Se, Te). The second group contains 26 crystals with the ternary composition (A’B’Q 2 ) (A’ = Ag, Cu, Au, Na; B’ = B, Al, Ga, In; Q = S, Se, Te). Among these 30 chalcogenide crystals, the results for 11 crystals: Tl 2 CdGeSe 4 , Tl 2 CdSnSe 4 , Tl 2 HgSiSe 4 , Tl 2 HgSnS 4 , AuBSe 2 , AuBTe 2 , AuAlTe 2 , AuGaTe 2 , AuInTe 2 , AgAlSe 2 , and AgAlTe 2 are revealed for the first time. In addition, temperature-dependent transport properties of pure and doped AgSbSe 2 and AgSbTe 2 crystals with dopant compositions of AgSb 0.94 Cd 0.06 Te 2 and AgSbTe 1.85 Se 0.15 were explored. These results provide an excellent database for bulk chalcogenides crucial for a wide range of potential applications in renewable energy fields.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Mutations of Omicron Variant at the Interface of the Receptor Domain Motif and Human Angiotensin-Converting Enzyme-2

The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with a large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense, and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and the human angiotensin-converting enzyme-2 (ACE2) interface, we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU) indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge, which facilitates the interaction with ACE2. We have identified changes in bonding due to mutations in the RBM. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

First-principles calculation of lattice distortions in four single phase high entropy alloys with experimental validation

Exceptional properties of high entropy alloys (HEAs) are attributed to the disordered random solid solution of multiple alloying elements. Despite numerous studies, the fundamental understanding at the electronic and atomic levels is still missing. We report a comparative study of four fcc HEAs of NiFeCoCr and NiFeCoCrX (X = Mn, Cu, or Pd) based on ab initio calculations using large supercells with 500 atoms in equal composition. After fully optimizing their structures using the VASP package, their electronic structure, interatomic bonding, partial charge distribution, and mechanical properties are calculated and compared, revealing the intricate interdependence among them. A novel parameter based on the quantum mechanical metric for internal cohesion, the total bond order density (TBOD), is used to interpret the calculated properties. The highest TBOD is found in Cantor alloy NiFeCoCrMn but lower in NiFeCoCrPd. The atomic radii vary depending on their local chemical environment. The resulting lattice distortions is validated experimentally in NiFeCoCrMn and NiFeCoCrPd. Moreover, modeling of Cu and Pd clustering in the supercell shows they have lower total energy in agreement with the observation of Cu-enhanced nano-participates in NiFeCoCrCu and Pd-induced concentration wave in NiFeCoCrPd HEAs.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Temperature-Dependent Properties of Molten Li 2 BeF 4 Salt Using Ab Initio Molecular Dynamics

Molten lithium tetrafluoroberyllate (Li 2 BeF 4 ) salt, also known as FLiBe, with a 2:1 mixture of LiF and BeF 2 is being proposed as a coolant and solvent in advanced nuclear reactor designs, such as the molten salt reactor or the fluoride salt cooled high-temperature reactor. We present the results on the structure and properties of FLiBe over a wide range of temperatures, 0–2000 K, from high-throughput ab initio molecular dynamics simulation using a supercell model of 504 atoms. The variations in the local structures of solid and liquid FLiBe with temperature are discussed in terms of a pair distribution function, coordination number, and bond angle distribution. The temperature-dependent electronic structure and optical and mechanical properties of FLiBe are calculated. The optical and mechanical property results are reported for the first time. The results above and below the melting temperature (~732 K) are compared with the experimental data and with data for crystalline FLiBe. The electronic structure and interatomic bonding results are discussed in correlation with the mechanical strength. A novel concept of total bond order density (TBOD), an important quantum mechanical parameter, is used to characterize the internal cohesion and strength in the simulated models. The results show a variation in the rate of change in properties in solid and liquid phases with anomalous behavior across the melting region. The observed trend is the decrease in mechanical strength, band gap, and TBOD in a nonlinear fashion as a function of temperature. The refractive index shows a surprising minimum at 850 K, among the tested temperatures, which lies above the melting point. These findings provide a new platform to understand the interplay between the temperature-dependent structures and properties of FLiBe salt.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Structural and physical properties of 99 complex bulk chalcogenides crystals using first-principles calculations

Chalcogenide semiconductors and glasses have many applications in the civil and military fields, especially in relation to their electronic, optical and mechanical properties for energy conversion and in enviormental materials. However, they are much less systemically studied and their fundamental physical properties for a large class chalcogenide semiconductors are rather scattered and incomplete. Here, we present a detailed study using well defined first-principles calculations on the electronic structure, interatomic bonding, optical, and mechanical properties for 99 bulk chalcogenides including thirteen of these crytals which have never been calculated. Due to their unique composition and structures, these 99 bulk chalcogenides are divided into two main groups. The first group contains 54 quaternary crystals with the structure composition (A2BCQ4) (A = Ag, Cu; B = Zn, Cd, Hg, Mg, Sr, Ba; C = Si, Ge, Sn; Q = S, Se, Te), while the second group contains scattered ternary and quaternary chalcogenide crystals with a more diverse composition (AxByCzQn) (A = Ag, Cu, Ba, Cs, Li, Tl, K, Lu, Sr; B = Zn, Cd, Hg, Al, Ga, In, P, As, La, Lu, Pb, Cu, Ag; C = Si, Ge, Sn, As, Sb, Bi, Zr, Hf, Ga, In; Q = S, Se, Te; x=1, 2, 3; y=0, 1, 2, 5; z=0, 1, 2 and n=3, 4, 5, 6, 9). Moreover, the total bond order density (TBOD) is used as a single quantum mechanical metric to characterize the internal cohesion of these crystals enabling us to correlate them with the calculated properties, especially their mechanical properties. This work provides a very large database for bulk chalcogenides crucial for the future theoretical and experimental studies, opening opportunities for study the properties and potential application of a wide variety of chalcogenides.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intramolecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

59 BASIC BIOLOGICAL SCIENCES↗