Mechanical Properties of a Solvated Biomolecule: RGD (1FUV) Peptide.

The mechanical properties of proteins/peptides play an essential role in their functionalities and implications, as well as their structure and dynamic properties. Understanding mechanical properties is pivotal to our knowledge of protein folding and the molecular basis of diverse cellular processes. Herein, we present a computational approach using ab initio quantum mechanical calculations to determine the mechanical properties-such as bulk modulus, shear modulus, Young's modulus, and Poisson's ratio-of a solvated Arg-Gly-Asp (RGD) peptide model. Since this peptide serves as the RGD-directed integrin recognition site and may participate in cellular adhesion, it is considered a promising small peptide for medicinal applications. This successful approach paves the way for investigating larger and more complex biomolecules.

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.

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.

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.

Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation.

The spike protein of SARS-CoV-2 binds to the ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analyses at molecular, amino acid (AA), and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex for SARS-CoV and SARS-CoV-2 with its Alpha and Beta variants. Our study uses the molecular dynamics (MD) simulations with the molecular mechanics generalized Born surface area (MM-GBSA) method to predict the binding free energy (BFE) and to determine the actual interacting AAs, as well as two ab initio quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q493, Y505, Q498, N501, T500, N487, Y449, F486, K417, Y489, F456, Y495, and L455 have been identified as hotspots in SARS-CoV-2 RBD, while those in ACE2 are K353, K31, D30, D355, H34, D38, Q24, T27, Y83, Y41, and E35. RBD with Alpha and Beta variants has slightly different interacting AAs due to N501Y mutation. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q493, Q498, N501, F486, K417, and F456 in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. RBD with the Alpha variant binds with ACE2 stronger than the wild-type RBD or Beta. In the Beta variant, K417N reduces the binding, E484K slightly enhances it, and N501Y significantly increases it as in Alpha. The DFT results reveal that N487, Q493, Y449, T500, G496, G446, and G502 in RBD of SARS2 form pairs via specific hydrogen bonding with Q24, H34, E35, D38, Y41, Q42, and K353 in ACE2.

Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding.

The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development.

Molecular mechanism and binding free energy of doxorubicin intercalation in DNA.

The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of ΔGele, ΔGvDW, ΔGpolar, ΔGnon-polar, TΔStotal, ΔGdeform, ΔGcon, and ΔGion. To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (ΔGdeform), the energy cost from translational and rotational entropic contributions (TΔStran+rot), the total electrostatic interactions (ΔGpolar-PB/GB + ΔGele) of incorporation, the intramolecular electrostatic interactions (ΔGele) and electrostatic polar solvation interactions (ΔGpolar-PB/GB) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (ΔGvDW), the non-polar solvation interaction (ΔGnon-polar), the vibrational entropic contribution (TΔSvib), and the standard concentration dependent free energies of DOX (ΔGcon) and the ionic solution (ΔGion). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX-DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. We have calculated the total binding free energy (BFE) (ΔGt-sim) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX-DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX-DNA1 and DOX-DNA2 in the 1 : 1 complex is -9.1 and -5.1 kcal mol-1 respectively. The same quantities from the modified MM-PBSA method are -12.74 and -8.35 kcal mol-1 respectively. The value of the total BFE ΔGt-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of -7.7 ± 0.3 kcal mol-1.

Deformation behavior of an amorphous zeolitic imidazolate framework - from a supersoft material to a complex organometallic alloy.

Zeolitic imidazolate frameworks (ZIFs)-a subset of metal-organic frameworks (MOFs)-have recently attracted immense attention. Many crystalline ZIFs (c-ZIFs) have highly porous zeolite structures that are ideal for molecular encapsulation. Recently emerging non-crystalline or amorphous ZIFs (a-ZIFs) with a similar short-range order are of interest because they can be converted from c-ZIFs for large-scale production. Here, we present a computational study of the deformation behavior of a unique a-ZIF model by simulating step-wise compression and expansion with strains between -0.389 and +0.376. An insulator-to-metal transition is observed at 51 GPa leading to a multicomponent light amorphous alloy of only 3.68 g (cm)-3. A high-density amorphous-to-amorphous phase transition is observed due to the sudden formation of N-N bond pairs. The systematic expansion of the a-ZIF retains the framework softness until it fractures at high strain. Based on the expansion data, we propose an empirical formula for super-soft materials, which is in line with available experimental data.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

The Hydration Effect and Selectivity of Alkali Metal Ions on Poly(ethylene glycol) Models in Cyclic and Linear Topology.

The effects of hydration and alkali metal ion (K+, Na+, Li+) bonding to two structural variants of poly(ethylene glycol) (PEG), viz., a cyclic (18-crown-6) configuration and a linear chain model with two different lengths, are studied by ab initio density functional theory calculations. A total of 24 structural models are constructed, with different conformations of the PEG chain and its molecular environment. Detailed comparisons of the results enable us to obtain conclusive evidence on the effects of the different components of the solution environment on the PEG structural variants in terms of the binding energy, partial charge distribution, solvation effect, interfacial hydrogen bonding, and cohesion between different structural units in the system composed of PEG, alkali metal ions, and water. On the basis of these comprehensive and precise comparisons, we conclude that the ion-PEG interaction is strongly influenced by the presence of solvent and that the charge transfer in the PEG complex depends crucially on its topology, the type of alkali metal ion, and the solvent. The interaction between alkali metal ions in the two PEG models does not always scale with the ion size but depends on their local environment.

Metallic Ternary Telluride with Sphalerite Superstructure.

A new ternary compound with composition Cu5Sn2Te7 has been synthesized using the stoichiometric reaction of Cu, Sn, and Te. The compound crystallizes in C2 space group with unit cell parameters of a = 13.549(2) Å, b = 6.0521(11) Å, c = 9.568(2) Å, and ß = 98.121(2)°. Cu5Sn2Te7 is a superstructure of sphalerite and exhibits tetrahedral coordination of Cu, Sn, and Te atoms, containing a unique adamantane-like arrangement. The compound is formally mixed valent with a high electrical conductivity of 9.8 × 10(5) S m(-1) at 300 K and exhibits metallic behavior having p-type charge carriers as indicated from the positive Seebeck coefficient. Hall effect measurements further confirm holes as charge carriers with a carrier density of 1.39 × 10(21) cm(-3) and Hall mobility of 4.5 cm(2) V(-1) s(-1) at 300 K. The electronic band structure calculations indicate the presence of a finite density of states around the Fermi level and agree well with the p-type metallic conductivity. Band structure analysis suggests that the effective mass of the hole state is small and could be responsible for high electronic conductivity and Hall mobility. The high thermal conductivity of 15.1 W m(-1) K(-1) at 300 K coupled with the low Seebeck coefficient results in a poor thermoelectric figure of merit (ZT) for this compound. Theoretical calculations indicate that if Cu5Sn2Te7 is turned into a valence precise compound by substituting one Cu by a Zn, a semiconducting material, Cu4ZnSn2Te7, with a direct band gap of ∼ 0.5 eV can be obtained.

Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA.

We present a first-principles density functional study elucidating the effects of solvent, metal ions and topology on the electronic structure and hydrogen bonding of 12 well-designed three dimensional G-quadruplex (G4-DNA) models in different environments. Our study shows that the parallel strand structures are more stable in dry environments and aqueous solutions containing K(+) ions within the tetrad of guanine but conversely, that the anti-parallel structure is more stable in solutions containing the Na(+) ions within the tetrad of guanine. The presence of metal ions within the tetrad of the guanine channel always enhances the stability of the G4-DNA models. The parallel strand structures have larger HOMO-LUMO gaps than antiparallel structures, which are in the range of 0.98 eV to 3.11 eV. Partial charge calculations show that sugar and alkali ions are positively charged whereas nucleobases, PO4 groups and water molecules are all negatively charged. Partial charges on each functional group with different signs and magnitudes contribute differently to the electrostatic interactions involving G4-DNA and favor the parallel structure. A comparative study between specific pairs of different G4-DNA models shows that the Hoogsteen OH and NH hydrogen bonds in the guanine tetrad are significantly influenced by the presence of metal ions and water molecules, collectively affecting the structure and the stability of G4-DNA.

Electronic structure and partial charge distribution of Doxorubicin in different molecular environments.

The electronic structure and partial charge of doxorubicin (DOX) in three different molecular environments-isolated, solvated, and intercalated in a DNA complex-are studied by first-principles density functional methods. It is shown that the addition of solvating water molecules to DOX, together with the proximity to and interaction with DNA, has a significant impact on the electronic structure as well as on the partial charge distribution. Significant improvement in estimating the DOX-DNA interaction energy is achieved. The results are further elucidated by resolving the total density of states and surface charge density into different functional groups. It is concluded that the presence of the solvent and the details of the interaction geometry matter greatly in determining the stability of DOX complexation. Ab initio calculations on realistic models are an important step toward a more accurate description of the long-range interactions in biomolecular systems.

van der Waals Interactions on the Mesoscale: Open-Science Implementation, Anisotropy, Retardation, and Solvent Effects.

The self-assembly of heterogeneous mesoscale systems is mediated by long-range interactions, including van der Waals forces. Diverse mesoscale architectures, built of optically and morphologically anisotropic elements such as DNA, collagen, single-walled carbon nanotubes, and inorganic materials, require a tool to calculate the forces, torques, interaction energies, and Hamaker coefficients that govern assembly in such systems. The mesoscale Lifshitz theory of van der Waals interactions can accurately describe solvent and temperature effects, retardation, and optically and morphologically anisotropic materials for cylindrical and planar interaction geometries. The Gecko Hamaker open-science software implementation of this theory enables new and sophisticated insights into the properties of important organic/inorganic systems: interactions show an extended range of magnitudes and retardation rates, DNA interactions show an imprint of base pair composition, certain SWCNT interactions display retardation-dependent nonmonotonicity, and interactions are mapped across a range of material systems in order to facilitate rational mesoscale design.

Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence.

The role of base pair composition and stacking sequence in the optical properties and electronic transitions of DNA is of fundamental interest. We present and compare the optical properties of DNA oligonucleotides (AT)10, (AT)5(GC)5, and (AT-GC)5 using both ab initio methods and UV-vis molar absorbance measurements. Our data indicate a strong dependence of both the position and intensity of UV absorbance features on oligonucleotide composition and stacking sequence. The partial densities of states for each oligonucleotide indicate that the valence band edge arises from a feature associated with the PO4(3-) complex anion, and the conduction band edge arises from anti-bonding states in DNA base pairs. The results show a strong correspondence between the ab initio and experimentally determined optical properties. These results highlight the benefit of full spectral analysis of DNA, as opposed to reductive methods that consider only the 260 nm absorbance (A260) or simple purity ratios, such as A260/A230 or A260/A280, and suggest that the slope of the absorption edge onset may provide a useful metric for the degree of base pair stacking in DNA. These insights may prove useful for applications in biology, bioelectronics, and mesoscale self-assembly.

Densification of a continuous random network model of amorphous SiO2 glass.

We have investigated the mechanism of densification of a nearly perfect continuous random network (CRN) model of amorphous SiO2 (a-SiO2) glass with 1296 atoms and periodic boundary conditions. The model has no under- or over-coordinated atoms and small bond length and bond angle distributions. This near-perfect model is systematically densified up to a pressure of 80 GPa using ab initio constant-pressure technique. By assessing a full spectrum of properties including atomic structure, bonding characteristics, effective charges, bond order values, electron density of states, localization of wave functions, elastic and mechanical properties, and interband optical absorption at each pressure, we reveal the pertinent details on the structural, mechanical and optical characteristics of the glass model under pressure. They all confirm the central theme that amorphous to amorphous phase transformation (AAPT) from a low-density state to a high-density state is at a pressure between 20 and 35 GPa in this nearly ideal a-SiO2 network. This pressure range represents an upper limit for such a transition in vitreous silica. The phase transformation roots from the change of Si-O bonding from a mixture of ionic and covalent nature at low pressure to a highly covalent bonding under high pressure. In addition, the calculated theoretical refractive index of the glass model as a function of the pressure is reported for the first time and in good agreement with the available experimental data.

High-resolution spectroscopy of bonding in a novel BeP2N4 compound.

The recently discovered compound BeP2N4 that crystallizes in the phenakite-type structure has potential application as a high strength optoelectronic material. Therefore, it is important to analyze experimentally the electronic structure, which was done in the present work by monochromated electron energy-loss spectroscopy. The detection of Be is challenging due to its low atomic number and easy removal under electron bombardment. We were able to determine the bonding behavior and coordination of the individual atomic species including Be. This is evident from a good agreement between experimental electron energy-loss near-edge structures of the Be-K-, P-L2,3-, and N-K-edges and density functional theory calculations.

Effects of Na/K-Cl Salts on Hydrolysis of Aluminosilicate Glass Using Ab Initio Molecular Dynamics.

The structural and chemical modifications on the surface of pure and alkali-doped aluminosilicate (AS) glasses due to hydrolysis are investigated using ab initio molecular dynamics. The effects of water on the glass network are fully elucidated by analyzing the short- and intermediate-range structural orders embedded in the pair distribution function, bond length and angle distribution, coordination number, and interatomic bonding. A novel concept of total bond order is used to quantify and compare the strength of bonds in hydrated and unhydrated glasses. We show that AS glass is hydrolyzed by water diffusion near the surface and by proton (H+) transfers into the bulk, which increases with time. Hence, a dissolved glass-water interface becomes rich in Si-OH and Al-OH. The alkali ions associated with the nonbridging oxygen accelerate the hydrolysis by facilitating water and H+ diffusion. Al is more impacted by hydrolysis than Si, resulting in greater variation in the Al-O bond order than Si-O. Doping of NaCl and KCl enhances the ionization of water and the hydrolysis of ASs with increased salt concentration. The KCl doping ionizes more water molecules and causes more degradation of the glass network than NaCl. Co-doping of Na and K results in a mixed alkali effect due to complex interatomic bonding from different-sized ions. These exceptionally detailed findings in highly complex glasses with varying salt compositions provide new and unprecedented atomistic insights that can help to understand the hydrolysis and dissolution mechanisms of ASs and other silicate glasses.

Impact of BA.1, BA.2, and BA.4/BA.5 Omicron mutations on therapeutic monoclonal antibodies.

The emergence of Omicron SARS-CoV-2 subvariants (BA.1, BA.2, BA.4, and BA.5), with an unprecedented number of mutations in their receptor-binding domain (RBD) of the spike-protein, has fueled a resurgence of COVID-19 infections, posing a major challenge to the efficacy of existing vaccines and monoclonal antibody (mAb) therapeutics. We conducted a systematic molecular dynamics (MD) simulation to investigate how the RBD mutations of these subvariants affect the interactions with broad mAbs including AstraZeneca (COV2-2196 and COV2-2130), Brii Biosciences (BRII-196), Celltrion (CT-P59), Eli Lilly (LY-CoV555 and LY-CoV016), Regeneron (REGN10933 and REGN10987), Vir Biotechnology (S309), and S2X259. Our results show a complete loss of binding for COV2-2196, BRII-196, CT-P59, and LY-CoV555 with all Omicron RBDs. Additionally, REGN10987 totally loses its binding with BA.1, but retains a partial binding with BA.2 and BA.4/5. The binding reduction is significant for LY-CoV016 and REGN10933 but moderate for COV2-2130. S309 and S2X259 retain their binding with BA.1 but exhibit decreased binding with other subvariants. We introduce a mutational escape map for each mAb to identify the key RBD sites and the corresponding critical mutations. Overall, our findings suggest that the majority of therapeutic mAbs have diminished or missing activity against Omicron subvariants, indicating the urgent need for a new therapeutic mAb with a better design.

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: Pb0.99-ySb0.012SnySe1-2xTexSx (x = 0.1, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, and y = 0) and Pb0.99-ySb0.012SnySe1-2xTexSx (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 (ΘD), thermal conductivity (κ), Grüneisen parameter (γα), dominant phonon wavelength (λdom), and melting temperature (Tm). We find that the lattice thermal conductivity is significantly reduced when GeTe is alloyed into the following compositions: Ge0.75Sb0.13Pb0.12Te, Ge0.61Ag0.11Sb0.13Pb0.12Bi0.01Te, and Ge0.61Ag0.11Sb0.13Pb0.12Mn0.05Bi0.01Te. This reduction is due to the mass increase and strain fluctuations. The results also show that Ge0.61Ag0.11Sb0.13Pb0.12Bi0.01Te 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, Ge0.61Ag0.11Sb0.13Pb0.12Bi0.01Te has the highest Grüneisen parameter with a reduced and temperature-independent lattice thermal conductivity. The positive correlation between ΘD 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 ΘD, and a lower lattice thermal conductivity.