All-Atom Force Field for Molecular Dynamics Simulations on Organotransition Metal Solids and Liquids. Application to M(CO)n (M = Cr, Fe, Ni, Mo, Ru, or W) Compounds

Synthesis and Volatility Characterization of Mo(II) and W(II) Compounds for Thin Films

Mo(II) and W(II) compounds, Mo(η3-allyl)(CO)2(Tri-MEDA)Br (1), Mo(η3-allyl)(CO)2(TMEDA)Br (2), W(η3-allyl)(CO)2(Tri-MEDA)Br (3), and W(η3-allyl)(CO)2(TMEDA)Br (4) (Tri-MEDA = N,N,N'-trimethylethylenediamine), were synthesized and characterized. The molecular structures of 1 and 3 were nearly identical with a pseudo-octahedral geometry except for the different Mo and W metal centers. The thermogravimetric analysis of 1 and 3 showed approximately 53 and 64% residues at 550 °C, respectively, which were significantly higher than the values for the expected materials. However, 1 and 3 sublimed at 100 °C under 0.40 Torr and 120 °C under 0.50 Torr, respectively, confirming that they were volatile. For 1 and 3, the temperatures at a vapor pressure of 1 Torr and enthalpies of vaporization (ΔHvap) were 168.78 °C and 143.8 kJ mol-1, and 167.48 °C and 148.5 kJ mol-1, respectively. The tungsten compound (3) exhibited good durability for 5 weeks under a thermal stability test at a sublimation temperature of 120 °C.

Theoretical investigation of solvent and oxidation/deprotonation effects on the electronic structure of a mononuclear Ru-aqua-polypyridine complex in aqueous solution

Mononuclear polypyridine ruthenium (Ru) complexes can catalyze various reactions, including water splitting, and can also serve as photosensitizers in solar cells. Despite recent progress in their synthesis, accurately modeling their physicochemical properties, particularly in solution, remains challenging. Herein, we conduct a theoretical investigation of the structural and electronic properties of a mononuclear Ru-aqua polypyridine complex in aqueous solution, considering five of its possible oxidation/protonation states species: [RuII(H2O)(py)(bpy)2]2+, [RuII(OH)(py)(bpy)2]+, [RuIII(H2O)(py)(bpy)2]3+, [RuIII(OH)(py)(bpy)2]2+ and [RuIV(O)(py)(bpy)2]2+, where py = pyridine and bpy = 2,2'-bipyridine. At first, we investigate the impact of proton-coupled and non-coupled electron transfer reactions on the geometry and electronic structure of the complexes in vacuum and in solution, using an implicit solvent model. Then, using a sequential multiscale approach that combines quantum mechanics and molecular mechanics (S-QM/MM), we examine the explicit solvent effects on the electronic excitations of the complexes, and compare them with the experimental results. The complexes were synthesized, and their absorption spectra measured in aqueous solution. To accurately describe the QM interactions between the metal center and the aqueous ligand in the MM simulations, we developed new force field parameters for the Ru atom. We analyze the solvent structure around the complexes and account for its explicit influence on the polarization and electronic excitations of the complexes. Notably, accounting for the explicit solvent polarization effects of the first solvation shells is essential to correctly describe the energy of the electronic transitions, and the explicit treatment of the hydrogen bonds at the QM level in the excitation calculations improves the accuracy of the description of the metal-to-ligand charge-transfer bands. Transition density matrix analysis is used to characterize all electronic transitions in the visible and ultraviolet ranges according to their charge-transfer (CT) character. This study elucidates the electronic structure of those ruthenium polypyridyl complexes in aqueous solution and underscores the importance of precisely describing solvent effects, which can be achieved employing the S-QM/MM method.

Visualizing interfacial collective reaction behaviour of Li-S batteries

Benefiting from high energy density (2,600 Wh kg-1) and low cost, lithium-sulfur (Li-S) batteries are considered promising candidates for advanced energy-storage systems1-4. Despite tremendous efforts in suppressing the long-standing shuttle effect of lithium polysulfides5-7, understanding of the interfacial reactions of lithium polysulfides at the nanoscale remains elusive. This is mainly because of the limitations of in situ characterization tools in tracing the liquid-solid conversion of unstable lithium polysulfides at high temporal-spatial resolution8-10. There is an urgent need to understand the coupled phenomena inside Li-S batteries, specifically, the dynamic distribution, aggregation, deposition and dissolution of lithium polysulfides. Here, by using in situ liquid-cell electrochemical transmission electron microscopy, we directly visualized the transformation of lithium polysulfides over electrode surfaces at the atomic scale. Notably, an unexpected gathering-induced collective charge transfer of lithium polysulfides was captured on the nanocluster active-centre-immobilized surface. It further induced an instantaneous deposition of nonequilibrium Li2S nanocrystals from the dense liquid phase of lithium polysulfides. Without mediation of active centres, the reactions followed a classical single-molecule pathway, lithium polysulfides transforming into Li2S2 and Li2S step by step. Molecular dynamics simulations indicated that the long-range electrostatic interaction between active centres and lithium polysulfides promoted the formation of a dense phase consisting of Li+ and Sn2- (2 < n ≤ 6), and the collective charge transfer in the dense phase was further verified by ab initio molecular dynamics simulations. The collective interfacial reaction pathway unveils a new transformation mechanism and deepens the fundamental understanding of Li-S batteries.

Identification of high-affinity pyridoxal kinase inhibitors targeting cancer therapy: an integrated docking and molecular dynamics simulation approach

Pyridoxal kinase (PDXK) is a vitamin B6-dependent transferase enzyme encoded by the PDXK gene, crucial for leukemic cell proliferation. Disruption of its activity causes altered metabolism and reduced levels of nucleotides and polyamines. PDXK and pyridoxal 5'-phosphate (PLP) are overexpressed in various carcinomas, making them promising targets for drug design against cancer. Targeting PDXK may hold promise as a therapeutic approach for cancer treatment. This study focused on discovering potential inhibitors that could selectively interrupt the binding of pyridoxal phosphate (PLP) to pyridoxal kinase (PDXK). A commercially available library of 7,28,747 natural and druglike compounds was virtually screened using a molecular docking approach to target the substrate binding pocket of PDXK. Six promising inhibitors were identified, and all-atom molecular dynamics simulations were conducted on the PDXK-ligand complexes for 100 ns to assess their binding conformational stability. The simulation results indicated that the binding of ZINC095099376, ZINC01612996, ZINC049841390, ZINC095098959, ZINC01482077, and ZINC03830976 induced a slight structural change and stabilized the PDXK structure. This analysis provided valuable information about the critical residues involved in the PDXK-PLP complex formation and can be utilized in designing specific and effective PDXK inhibitors. According to this study, these compounds could be developed as anticancer agents targeting PDXK as a potential candidate for further study.Communicated by Ramaswamy H. Sarma.

Phytochemical Moieties From Indian Traditional Medicine for Targeting Dual Hotspots on SARS-CoV-2 Spike Protein: An Integrative in-silico Approach

SARS-CoV-2 infection across the world has led to immense turbulence in the treatment modality, thus demanding a swift drug discovery process. Spike protein of SARS-CoV-2 binds to ACE2 receptor of human to initiate host invasion. Plethora of studies demonstrate the inhibition of Spike-ACE2 interactions to impair infection. The ancient Indian traditional medicine has been of great interest of Virologists worldwide to decipher potential antivirals. Hence, in this study, phytochemicals (1,952 compounds) from eight potential medicinal plants used in Indian traditional medicine were meticulously collated, based on their usage in respiratory disorders, along with immunomodulatory and anti-viral potential from contemporary literature. Further, these compounds were virtually screened against Receptor Binding Domain (RBD) of Spike protein. The potential compounds from each plant were prioritized based on the binding affinity, key hotspot interactions at ACE2 binding region and glycosylation sites. Finally, the potential hits in complex with spike protein were subjected to Molecular Dynamics simulation (450 ns), to infer the stability of complex formation. Among the compounds screened, Tellimagrandin-II (binding energy of −8.2 kcal/mol and binding free energy of −32.08 kcal/mol) from Syzygium aromaticum L. and O-Demethyl-demethoxy-curcumin (binding energy of −8.0 kcal/mol and binding free energy of −12.48 kcal/mol) from Curcuma longa L. were found to be highly potential due to their higher binding affinity and significant binding free energy (MM-PBSA), along with favorable ADMET properties and stable intermolecular interactions with hotspots (including the ASN343 glycosylation site). The proposed hits are highly promising, as these are resultant of stringent in silico checkpoints, traditionally used, and are documented through contemporary literature. Hence, could serve as promising leads for subsequent experimental validations.

Magnetic Field Triggerable Macroporous PDMS Sponge Loaded with an Anticancer Drug, 5-Fluorouracil

This study aims to prepare, optimize, and characterize magnetic-field-sensitive sugar-templated polydimethylsiloxane (PDMS) sponges for localized delivery of an anticancer drug, 5-fluorouracil (FLU). For this purpose, different concentrations of carbonyl iron (CI) and magnetite Fe₃O₄ nanopowders were embedded as magnetosensitive materials in PDMS resins for the fabrication of macroporous sponges via a sugar-template process. The process is environmentally friendly and simple. The fabricated interconnected macroporous magnetic particles loaded PDMS sponges possess flexible skeletons and good recyclability because of their recoverability after compression (deformation) without any breakdown. The prepared magnetic PDMS sponges were evaluated for their morphology (SEM and EDS), porosity (absorbency), elastic modulus, deformation under a magnetic field, thermostability, and in vitro cell studies. All physicochemical and magnetomechanical analysis confirmed that the optimized magnetic-field-sensitive PDMS sponge can provide an efficient method for delivering an on-demand dose of anticancer drug solutions at a specific location and timing with the aid of controlled magnetic fields.

Enhancement of interface thermal conductance between Cr-Ni alloy and dielectric via Cu nano-interlayer

Facilitating interfacial thermal transport is highly desirable for various engineering applications, such as improving heat dissipation in microelectronics and efficiency of electrothermal heating element. Here, the interface thermal conductances (ITCs) of Cr0.22Ni0.78/MgO and Cr0.22Ni0.78/Al2O3interfaces are studied through the non-equilibrium molecular dynamics simulation. It is found that the two ITCs can be hugely enhanced by 3 and 2.4 times, respectively, with the introduction of Cu nano-interlayer of a thickness larger than 7.2 Å. The enhanced ratio is robust and shows weak dependence on temperature. Further vibrational spectral analysis and phonon transmission function reveal that the enhancement in ITC mainly originates from the boosting of inelastic phonon scattering, which is generally considered to contribute a small proportion to ITC. Here, the inelastic scattering contributes as high as 63% to the ITC of Cr0.22Ni0.78/Cu/MgO interface at 300 K. The findings provide an effective strategy to enhance ITC at a wide temperature range and advance our understanding of inelastic scattering in interfacial phonon transport.

The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective

Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO₂, SO₂ and NO₂ that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ₄₂ peptide due to its interaction of toxic gas (CO, CO₂, SO₂ and NO₂). During the 400 ns simulation, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes have smaller Root Mean Square Deviation values when compared to the Aβ₄₂ peptide, which shows that the interaction of toxic gases (CO, CO₂, SO_2, and NO₂) would increase the Aβ₄₂ peptide structural stability. The radius of gyration analysis also supports that Aβ₄₂ interacted CO₂ and SO₂ complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ₄₂ interacted CO₂ and SO₂ complexes have a greater compact structure in comparison to Aβ₄₂ interacted CO and NO₂ complexes. Furthermore, all the Aβ₄₂ interacted toxic gas (CO, CO₂, SO_2, and NO₂) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ₄₂.

In silico studies of the inhibition mechanism of dengue with papain

Dengue virus is becoming a major global disease; the envelope protein is the major target for vaccine development against Dengue. Nowadays, the attention has focused on developing inhibitors based on Papain is a promising target for treating Dengue. In the present work, the theoretical studies of E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and His159) complexes are analysed by Density Functional Theory (M06-2X/cc-pVDZ) method. Among the E-protein(Cys74-Glu79;Lys110)…Papain(Cys25, Asn175 and Hys159) complexes, E-protein(Glu76)…Papain(Cys25) complex has the highest interaction value of -352.22 kcal/mol. Moreover, the natural bond orbital analysis also supports the above results. The 100 ns Molecular Dynamics simulation reveals that, E-protein(Ala54-Ile129)…Papain(Cys25) complex had the lowest root mean square deviation value of 1 Å compared to the E-protein(Ala54-Ile129)… Papain(Asn175 & His159) complexes. The salt bridge formation between the Asp103 and Lys110 residues are the important stabilizing factor in E-protein(Ala54-Ile129)…Papain(Cys25) complex. This result can extend our knowledge of the functional behaviour of Papain and provides structural insight to target Envelope protein as forthcoming drug targets in Dengue.

Coagulation mechanisms of humic acid in metal ions solution under different pH conditions: A molecular dynamics simulation

Humic acid (HA) exerts a variety of significant environmental and geochemical influences on the soils, sediments and aqueous environments. The interaction with metal ions induces strong HA-metal complexation, thus effecting the transport of the toxic metals as well as the colloidal aggregation of HA. In the present work, we systematically report and analyze the aggregation mechanisms of HAs in solutions filled with different heavy cations (Ag⁺, Cd²⁺ and Cr³⁺) or common metal ions (Na⁺, Ca²⁺ and Al³⁺) under neutral and low pH conditions by using molecular dynamic simulations. We aim to explore the effects of pH, metal ions type and other possible weak interactions on the aggregation capabilities of HA. Scrutiny of the simulation results showed that the aggregation of HAs under neutral condition was driven by the HA-metal complexation which combined the effects of electrostatic attraction and inter-molecular bridging between cations and COO^- groups. Larger extent of aggregation was found in heavy metal ions compared with the common ones. On the other hand, under low pH condition, due to the protonation states of carboxyl and phenolic group, the aggregation of HAs was stabilized mainly by weak forces, such as hydrogen bonds between different functional groups. In addition, other weak interactions such as the hydrophilic and hydrophobic effects, the cation-π interactions have also been proposed to be progressive effects on the coagulation behavior. Our computational studies give supplement to the experimental observation and provide insights into the intrinsic mechanisms of the aggregation behavior of HAs and their complexation with metal ions. Such computational modelling supplied a highly effective tool for qualitatively evaluating their roles in environmental remediation.

Non-equilibrium adatom thermal state enables rapid additive nanomanufacturing

A new state of radical thermal non-equilibrium in surface adsorbed molecules is discovered that enables rapid surface diffusion of energized adatoms with a negligible effect on the substrate surface temperature. Due to enhanced surface diffusion, growth rates can be achieved that improve the feasibility of many nanofabrication techniques. Since the adatom temperature cannot be directly measured without disturbing its thermodynamic state, the first principle hard-cube model is used to predict both the adatom effective temperature and the surface temperature in response to gaseous particle impingement in a vacuum. The validity of the approach is supported by local, spatially-resolved surface temperature measurements of the thermal response to supersonic microjet gas impingement. The ability to determine and control the adatom effective temperature, and therefore the surface diffusion rate, opens new degrees of freedom in controlling a wide range of nanofabrication processes that critically depend on surface diffusion of precursor molecules. This fundamental understanding has the potential to accelerate research into nanoscale fabrication and to yield the new materials with unique properties that are only accessible with nanoscale features.

Modeling Halogen Bonds in Ionic Liquids: A Force Field for Imidazolium and Halo-Imidazolium Derivatives

In this work, a force field for molecular dynamics and Monte Carlo simulations of ionic liquids containing imidazolium and halo-imidazolium derivatives is presented. This force field is an extension of the well-known CL&P and OPLS-AA models and was validated by comparing predicted crystalline structures for 22 ionic liquid compounds with the corresponding data deposited at the Cambridge Structural Database. The obtained results indicate that the proposed force field extension allows the reproduction of the crystal data with an absolute average deviation lower than 2.4%. Finally, it was also established that the halogen atoms covalently bound to the studied imidazolium cations are positively charged and do not exhibit a so-called σ-hole feature. For this reason, the formation of halogen bonds in the proposed force field appears naturally from the parametrized atomic point-charge distribution, without the necessity of any extra interaction sites.

Atomistic Modelling of Confined Polypropylene Chains between Ferric Oxide Substrates at Melt Temperature

The interactions and conformational characteristics of confined molten polypropylene (PP) chains between ferric oxide (Fe₂O₃) substrates were investigated by molecular dynamics (MD) simulations. A comparative analysis of the adsorbed amount shows strong adsorption of the chains on the high-energy surface of Fe₂O₃. Local structures formed in the polymer film were studied utilizing density profiles, orientation of bonds, and end-to-end distance of chains. At interfacial regions, the backbone carbon-carbon bonds of the chains preferably orient in the direction parallel to the surface while the carbon-carbon bonds with the side groups show a slight tendency to orient normal to the surface. Based on the conformation tensor data, the chains are compressed in the normal direction to the substrates in the interfacial regions while they tend to flatten in parallel planes with respect to the surfaces. The orientation of the bonds as well as the overall flattening of the chains in planes parallel to the solid surfaces are almost identical to that of the unconfined PP chains. Also, the local pressure tensor is anisotropic closer to the solid surfaces of Fe₂O₃ indicating the influence of the confinement on the buildup imbalance of normal and tangential pressures.

Solvent effects on the polar network of ionic liquid solutions

Molecular dynamics simulations were used to probe mixtures of ionic liquids (ILs) with common molecular solvents. Four types of systems were considered: (i) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide plus benzene, hexafluorobenzene or 1,2-difluorobenzene mixtures; (ii) choline-based ILs plus ether mixtures (iii) choline-based ILs plus n-alkanol mixtures; and (iv) 1-butyl-3-methylimidazolium nitrate and 1-ethyl-3-methylimidazolium ethyl sulfate aqueous mixtures. The results produced a wealth of structural and aggregation information that highlight the resilience of the polar network of the ILs (formed by clusters of alternating ions and counter-ions) to the addition of different types of molecular solvent. The analysis of the MD data also shows that the intricate balance between different types of interaction (electrostatic, van der Waals, H-bond-like) between the different species present in the mixtures has a profound effect on the morphology of the mixtures at a mesoscopic scale. In the case of the IL aqueous solutions, the present results suggest an alternative interpretation for very recently published x-ray and neutron diffraction data on similar systems.

Evaluation of the OPLS-AA force field for the study of structural and energetic aspects of molecular organic crystals

Motivated by the need for reliable experimental data for the assessment of theoretical predictions, this work proposes a data set of enthalpies of sublimation determined for specific crystalline structures, for the validation of molecular force fields (FF). The selected data were used to explore the ability of the OPLS-AA parametrization to investigate the properties of solid materials in molecular dynamics simulations. Furthermore, several approaches to improve this parametrization were also considered. These modifications consisted in replacing the original FF atomic point charges (APC), by values calculated using quantum chemical methods, and by the implementation of a polarizable FF. The obtained results indicated that, in general, the best agreement between theoretical and experimental data is found when the OPLS-AA force field is used with the original APC or when these are replaced by ChelpG charges, computed at the MP2/aug-cc-pVDZ level of theory, for isolated molecules in the gaseous phase. If a good description of the energetic relations between the polymorphs of a compound is required then either the use of polarizable FF or the use of charges determined taking into account the vicinity of the molecules in the crystal (combining the ChelpG and MP2/cc-pVDZ methods) is recommended. Finally, it was concluded that density functional theory methods, like B3LYP or B3PW91, are not advisable for the evaluation of APC of organic compounds for molecular dynamic simulations. Instead, the MP2 method should be considered.

Modeling the structure and thermodynamics of ferrocenium-based ionic liquids

A new force-field for the description of ferrocenium-based ionic liquids is reported. Their unique nanostructure is probed by MD simulations.