Molecular Dynamics Investigation Research Articles

Integrating Mathematical and Computational Biochemistry with an Exploration of the Toxicological and Physical Dimensions of Novichok Agents: A QSAR and Molecular Dynamics Investigation

In recent decades, and particularly over the last few years, nerve agents have emerged as an ongoing threat yet to be neutralized. Specifically, Novichok, also known as A-class nerve agents, poses a significant risk to civilization due to the potential for terrorism and asymmetric threats. In the present study, we present results on toxicological properties, including calculated lipophilicity through QSAR analysis, as well as an array of physical and dynamic properties estimated via Molecular Dynamics Simulations.

A Coarse-Grained Molecular Dynamics Perspective on the Release of 5-Fluorouracil from Liposomes.

Liposomes, small bilayer phospholipid-containing vesicles, are frequently used to ensure slow drug release for a prolonged and improved therapeutic effect. Nevertheless, current findings on the membrane affinity and permeability of the anticancer agent 5-fluorouracil (5-FU) are confounding, which leads to a lack of a clear understanding of how lipid composition impacts the distribution of 5-FU within liposomal structures and its delivery. In the current work, we report a comprehensive coarse-grained molecular dynamics (CGMD) investigation on the influence of cholesterol (CHOL) and the cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) on the partitioning of 5-FU in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) double-bilayer systems, as well as its in vitro release from liposomes with identical lipid compositions. Our results show that 5-FU tends to accumulate at the water-lipid interface, in the vicinity of polar headgroups, without partitioning in the hydrophobic tail region. At the same time, the presence of CHOL proportionally increases the distribution of this drug in the interbilayer aqueous space, decreasing the drug's affinity toward the membrane polar head region, while DOTAP has only a slight effect on drug distribution. Thus, it is expected that 5-FU will be released slower from CHOL-containing DPPC liposomes but not DOTAP-containing vesicles. However, in vitro release studies showed that the release kinetics of 5-FU from DPPC vesicles is not influenced by the presence of CHOL and that the incorporation of 10 mol % DOTAP leads to the best release profile for 5-FU, highlighting the complexity of nanocarrier drug release kinetics. We hypothesize that the initial rapid release seen in dialysis experiments is not related to drug membrane permeability but rather to 5-FU adsorbed on the outer surface of liposomes.

Molecular dynamics investigation of epoxy resin adsorption mechanisms on clay surfaces and the mechanical properties of epoxy resin-clay

The strength of natural clay can be improved with epoxy resins. However, nanoscale curing mechanisms remain poorly understood, which is essential for enhancing stability. In this study, molecular dynamics simulation was employed to calculate the quantity of interface hydrogen bonds, adsorption energy, radius of gyration, and mechanical properties of clay cured by diglycidyl ether of bisphenol-A epoxy resin (DGEBA), diglycidyl ether 4,4’-dihydroxy diphenyl sulfone (DGEDDS), and Aliphatic epoxidation of olefin resin (AEOR). Adsorption behavior and mechanical properties of the clay cured by three epoxy resins were investigated: (1) The chain structure of AEOR led to 18.2% more hydrogen bonds than DGEBA and 59.1% more than DGEDDS. (2) The simulated adsorption energies for DGEBA, DGEDDS, and AEOR with kaolinite were 92.59, 98.25, and 116.87 kcal·mol−1, respectively. (3) The bulk and shear modulus of kaolinite increased by 4.93% and 4.80% when using AEOR. The interface stability and mechanical properties of kaolinite were also improved through strong hydrogen bonds and high adsorption energy. (4) The improvement in Young’s modulus of kaolinite was most significant with AEOR, followed by DGEDDS. AEOR excelled in the Z direction, while DGEDDS excelled in the X and Y directions. This research provided a theoretical foundation to effectively improve the properties of clay using epoxy resins.

Molecular dynamics investigation of unsupported double-shock induced micro-jet behaviors in copper containing helium bubbles

Molecular dynamics investigation of unsupported double-shock induced micro-jet behaviors in copper containing helium bubbles

Ab Initio Molecular Dynamics Investigation of Water and Butanone Adsorption on UiO-66 with Defects.

Volatile organic compounds (VOCs) are harmful chemicals that are found in minute quantities in the atmosphere and are emitted from a variety of industrial and biological processes. They can be harmful to breathe or serve as biomarkers for disease detection. Therefore, capture and detection of VOCs is important. Here, we have examined if the Zr-based UiO-66 metal-organic framework (MOF) can be used to capture butanone─a well-known VOC. Toward that end, we have performed Born-Oppenheimer ab initio molecular dynamics (AIMD) at 300 and 500 K to probe the energetics and molecular interactions between butanone [CH3C(O)CH2CH3] and open-cage Zr-UiO-66. Such interactions were systematically interrogated using three MOF structures: defective MOF with a missing 1,4-benzene-dicarboxylate linker and two H2O; pristine MOF with two H2O; and pristine dry MOF. These structures were loaded with one and four molecules of butanone to examine the effect of concentration as well. One-molecule loading interacted favorably with the defective structure at 300 K, only. In comparison, interactions with four-molecule loading were energetically favorable for all conditions. Persistent hydrogen bonds between the O atom of butanone, H2O, and μ3-OH hydroxyl attachments at Zr nodes substantially contributed to the intermolecular interactions. At higher loadings, butanone also showed a pronounced tendency to diffuse into the adjoining cages of Zr-UiO-66. The effect of such movement on interaction energies was rationalized using simple statistical mechanics-based models of interacting and noninteracting gases. Broadly, we learn that the presence of prior moisture within the interstitial cages of Zr-UiO-66 significantly impacts the adsorption behavior of butanone.

Morphological Characterization and Molecular Dynamics Investigation of In-Situ Silica Nanoparticle-Reinforced Poly(Dimethylsiloxane) as a New Approach to Fouling-Release Coatings

To explore a better understanding of the features of poly(dimethylsiloxane) (PDMS)/silica nanocomposites as fouling-release coatings, a series of PDMS networks filled with silica nanoparticles synthesized in-situ was investigated using small angle x-ray scattering (SAXS) and dynamical mechanical analysis (DMA). Three hydroxyl-terminated (HT) PDMS with different molecular weights, 18,000, 49,000, and 79,000 g/mole, were considered for preparing the nanocomposites at the various weight ratios: 1, 3, and 5:1 of HT-PDMS to tetraethyl orthosilicate (TEOS) as a precursor to the in-situ formation of the nano-silica particles. Two different TEOS were used regarding their degree of polymerization: monomeric type (n∼1) and oligomeric type (n∼5). The small-scale structure of the silica domains was examined using SAXS while scanning electron microscopy (SEM) was used to investigate the large-scale structures of the silica domains. The SAXS data showed a bicontinuous array of aggregates. In addition, the glass transition and molecular dynamics in the nanocomposites were investigated using DMA. The sample including 20 wt% silica, exhibited two tan δ peaks. One was related to the usual polymer glass transition, while the other, occurring at a higher temperature, was attributed to the glass transitions associated with polymer chains in proximity to silica domains. The mobility of these polymer chains was diminished due to their interactions with the surface of the silica particles. This result demonstrated the existence of two types of physical and chemical interactions between the silica aggregates and PDMS chains.

Molecular dynamics investigation of nano-polishing on silicon carbide substrate with rough topography using a rotating diamond abrasive

To achieve low-damage polishing on silicon carbide substrates utilizing a rotating diamond abrasive, the molecular dynamics model for nano-polishing is established. The nano-polishing simulation of silicon carbide substrates with both smooth and rough topographies is conducted using the diamond abrasive at two different velocity ratios. The constructed MD models are compared with existing models to assess the influence of abrasive rotation and substrate topography. The results provide valuable insights into the nano-polishing. Firstly, improving substrate smoothness and increasing abrasive rotation can effectively reduce von Mises stress, force, temperature, and amorphous layer thickness. Secondly, the atomic motion within silicon carbide substrates is affected by abrasive rotation and substrate topography, thus altering the removal mechanism. Finally, the differences in friction coefficient between the constructed MD models and existing models arise from atomic adhesion and plie-up phenomena.

Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation.

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental force spectroscopy, often coarse graining procedures are employed. Here, building on a previous study, we apply the adaptive resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations using two model systems as examples: One system is the previously investigated calix[4]arene dimer that shows reversible one-step unfolding, and the other example is provided by a small peptide, a β-alanine octamer in methanol solvent. The mechanical unfolding of this peptide proceeds via a metastable intermediate and, therefore, represents a first step toward a complex unfolding pathway. We show that the average number of native contacts serves as a robust order parameter for the forced unfolding of this small peptide. In addition to increasing the complexity of the relevant conformational changes, we study the impact of the methodology used for coarse graining. Apart from the iterative Boltzmann inversion method, we apply an ideal gas approximation, and therefore, we replace the solvent by a non-interacting system of spherical particles. In all cases, we find excellent agreement between the results of FPMD simulations performed fully atomistically and those of the AdResS simulations also in the case of fast pulling. This holds for all details of the unfolding pathways, such as the distributions of the characteristic forces and also the sequence of hydrogen-bond opening in case of the β-alanine octamer. Therefore, the methodology is very well suited to simulate the mechanical unfolding of systems of experimental relevance.

Structural and Dynamical Properties of Nucleic Acid Hairpins Implicated in Trinucleotide Repeat Expansion Diseases.

Dynamic mutations in some human genes containing trinucleotide repeats are associated with severe neurodegenerative and neuromuscular disorders-known as Trinucleotide (or Triplet) Repeat Expansion Diseases (TREDs)-which arise when the repeat number of triplets expands beyond a critical threshold. While the mechanisms causing the DNA triplet expansion are complex and remain largely unknown, it is now recognized that the expandable repeats lead to the formation of nucleotide configurations with atypical structural characteristics that play a crucial role in TREDs. These nonstandard nucleic acid forms include single-stranded hairpins, Z-DNA, triplex structures, G-quartets and slipped-stranded duplexes. Of these, hairpin structures are the most prolific and are associated with the largest number of TREDs and have therefore been the focus of recent single-molecule FRET experiments and molecular dynamics investigations. Here, we review the structural and dynamical properties of nucleic acid hairpins that have emerged from these studies and the implications for repeat expansion mechanisms. The focus will be on CAG, GAC, CTG and GTC hairpins and their stems, their atomistic structures, their stability, and the important role played by structural interrupts.

A molecular dynamics investigation into the inhibitory function of hydroxypropyl-beta-cyclodextrin (HPBCD) in its interaction with amyloid-beta (Aβ) plaques near the cell membrane in the context of Alzheimer's disease.

Although Alzheimer`s disease has been known for a long time, it is interesting that scientists are still doing widespread research on it. Meanwhile, in parallel with experimental research, computational research is also yielding interesting results. In this study, we investigated the inhibitory behavior of hydroxypropyl-beta-cyclodextrin (HPBCD) drug candidates, which are more soluble than beta-cyclodextrin (BCD), using molecular dynamics simulations and compared them with AC0107 new drug. Parameters such as cell membrane stability, protein stability, drug inhibition rate, protein permeability, hydrogen bonding agents, the study of the energy content of interactions between different groups, and interactions between different species were of interest. The outcomes indicate that the drug candidate HPBCD has a role in inhibiting protein membrane penetration and has better performance than new AC0107 drug. In other words, HPBCD not only act as a drug carrier of Alzheimer's disease, but also as an inhibitor of it and can play a double role in its improvement.

Advances in timing and control of ultrafast molecular dynamics: from XUV to infrared

Abstract With the availability of modern laser and detection technologies, the investigation of ultrafast molecular dynamics induced by intense laser pulses has become a routine practice. In this Topical Review, we present a survey of recent progress in the timing and control of ultrafast molecular dynamics, encompassing processes initiated by both extreme ultraviolet and near infrared pulses. Prospects and perspectives of this field are given. This Review underscores the remarkable potential for further advances in understanding and harnessing ultrafast molecular processes.

Low-Cost Purpose-Built Ultra-Low-Field NMR Spectrometer.

Low-field NMR has emerged as a new analytical technique for the investigation of molecular structure and dynamics. Here, we introduce a highly integrated ultralow-frequency NMR spectrometer designed for the purpose of ultralow-field NMR polarimetry of hyperpolarized contrast media. The device measures 10 cm × 10 cm × 2.0 cm and weighs only 370 g. The spectrometer's aluminum enclosure contains all components, including an RF amplifier. The device has four ports for connecting to a high-impedance RF transmit-receive coil, a trigger input, a USB port for connectivity to a PC computer, and an auxiliary RS-485/24VDC port for system integration with other devices. The NMR spectrometer is configured for a pulse-wait-acquire-recover pulse sequence, and key sequence parameters are readily controlled by a graphical user interface (GUI) of a Windows-based PC computer. The GUI also displays the time-domain and Fourier-transformed NMR signal and allows autosaving of NMR data as a CSV file. Alternatively, the RS485 communication line allows for operating the device with sequence parameter control and data processing directly on the spectrometer board in a fully automated and integrated manner. The NMR spectrometer, equipped with a 250 ksamples/s 17-bit analog-to-digital signal converter, can perform acquisition in the 1-125 kHz frequency range. The utility of the device is demonstrated for NMR polarimetry of hyperpolarized 129Xe gas and [1-13C]pyruvate contrast media (which was compared to the 13C polarimetry using a more established technology of benchtop 13C NMR spectroscopy, and yielded similar results), allowing reproducible quantification of polarization values and relaxation dynamics. The cost of the device components is only ∼$200, offering a low-cost integrated NMR spectrometer that can be deployed as a plug-and-play device for a wide range of applications in hyperpolarized contrast media production─and beyond.

A molecular dynamics investigation of nano-twins and nano-precipitates effects in CoCrFeNi-based high-entropy alloys

Abstract This study systematically investigates the effects of twin boundaries and precipitates on the performance of CoCrFeNi HEAs matrix using molecular dynamics simulation methods. By constructing corresponding HEAs models and conducting simulations of their structural evolution and mechanical behavior at the nanoscale, the influence mechanisms of nanotwins (NTs) and nano-precipitates (NPs) on the mechanical properties of the material were explored through in-depth analysis of simulation results. The findings suggest that twin boundaries effectively impede the movement and slip of dislocations and stacking faults in the material. As a result, this enhances its mechanical properties and inhibits plastic deformation, ultimately improving its ductility. Meanwhile, precipitates also impact the material's performance, and the shape of precipitates may exert different effects on the material, while the phase interface between precipitates and the matrix can hinder the expansion of defects. The presence of twin boundaries can enhance the strengthening effect of precipitates, further improving the material's performance. This study provides a new perspective for understanding the relationship between the microstructure and mechanical properties of HEAs materials, offering important references for the design and optimization of HEAs materials.

Dynamic Evolution of Local Atomic Environments in a Cu66Zr34 Bulk Metallic Glass

This study presents a molecular dynamics (MD) investigation of the evolution of local atomic environments (LAEs) in a Cu66Zr34 bulk metallic glass (BMG), both at rest and under constant shear deformation. LAEs were characterized using Voronoi polyhedra analysis. Even in the absence of external load, LAEs frequently transformed into one another due to short-ranged atomic position fluctuations. However, as expected, each transition from one polyhedra to another was balanced by the reverse transition, thereby preserving the proportions of the different polyhedra. Cu-centered icosahedral LAEs were observed to preferentially transform into and from <1,0,9,3,0>, <0,1,10,2,0>, and <0,2,8,2,0> LAEs. Upon applying pure shear, the simulation box was first deformed in one direction up to a strain of 25% and then in the opposite direction to the same strain level. Shear deformation induced large nonaffine atomic displacements in the directions parallel to the shear, which were concentrated in specific regions of the BMG, forming band-like regions. From the onset, shear deformation led to the destabilization of Cu-centered icosahedral LAEs, as indicated by more frequent transitions to and from other polyhedra. Unlike other Cu-centered LAEs, icosahedra were also found to be more sensitive to yielding. The destruction of Cu-centered icosahedra was primarily a result of net transformations into <1,0,9,3,0> and <0,2,8,2,0> LAEs in the BMG subjected to pure shear, with a minor contribution of transformations involving the <0,1,10,2,0> polyhedra.

Surprising Dynamics Phenomena in the Diels-Alder Reaction of C60 Uncovered with AI.

We performed an extensive artificial intelligence-accelerated quasi-classical molecular dynamics investigation of the time-resolved mechanism of the Diels-Alder reaction of fullerene C60 with 2,3-dimethyl-1,3-butadiene. In a substantial fraction (10%) of reactive trajectories, the larger C60 noncovalently attracts the 2,3-dimethyl-1,3-butadiene long before the barrier so that the diene undergoes the series of complex motions including roaming, somersaults, twisting, and twisting somersaults around the fullerene until it aligns itself to pass over the barrier. These complicated processes could be easily missed in typically performed quantum chemical simulations with shorter and fewer trajectories. After the barrier is passed, the bonds take longer to form compared to the simplest prototypical Diels-Alder reaction of ethene with 1,3-butadiene despite high similarities in transition states and barrier widths evaluated with intrinsic reaction coordinate (IRC) calculations. C60 is mainly responsible for these differences as its reaction with 1,3-butadiene is similar to the reaction with 2,3-dimethyl-1,3-butadiene: the only substantial difference being that the extra methyl groups double the probability of the prolonged alignment phase in dynamics. These additional calculations of C60 with 1,3-butadiene could be performed via active learning more easily by reusing the data generated for the other two reactions, showing the potential for larger-scale exploration of the effects of different substrates in the same types of reactions.

Molecular dynamics investigation of IEPOX chemical behavior at the interface and in the bulk phase of acidic aerosols

Isoprene epoxydiol (IEPOX) is an important reactive gas-phase intermediate produced by the photooxidation of isoprene under low NOx conditions, playing a key role in the formation of secondary organic aerosols (SOA). Previous studies have mostly focused on the liquid-phase reactions of IEPOX within aerosols; however, interfacial heterogeneous chemical reactions are equally important in SOA formation. This study systematically explores the reaction mechanisms of IEPOX at the acidic aerosol interface and in the bulk phase using classical molecular dynamics (MD) and ab initio molecular dynamics simulations (AIMD). The study found that the free energy of IEPOX at the aerosol interface significantly decreases, indicating that interfacial heterogeneous chemical reactions are indispensable for the formation of IEPOX-derived SOA. The research reveals the formation pathways of 2-methyltetrols (2-MTO) and 1,3,4-trihydroxy-3-methylbutan-2-yl sulfates (2-MTOOS), finding that the protonation of the epoxy O atom and the cleavage of the C–O bond are the rate-controlling steps, while the nucleophilic addition is a spontaneous process. Through multiple sets of simulations, it was observed that the formation frequency of 2-MTO at the acidic aerosol interface and in the bulk phase reached 53.8%, significantly higher than the 30.8% of 2-MTOOS, which is consistent with field observation data. Additionally, through metadynamics (MTD) simulations, it was suggested that IEPOX could undergoes acid-catalyzed ring-opening reactions at the interface, potentially followed by the transfer of H atoms from primary alcohols into the aerosol, leading to the possible formation of the intermediate product 3-methylbut-3-ene-1,2,4-triol (one of the proposed structures of C5-alkene triols). These findings provide new insights into the formation mechanism of IEPOX-derived SOA and offer a scientific basis for future studies on their physicochemical properties and atmospheric fate.

Atomistic insight into structure and properties of oxide films formed upon oxidation of Al–Mg alloys – reactive molecular dynamics study

Oxidation phenomena on metal surfaces can be advanced using atomistic modeling for the study of the structure and properties of the growing oxide films. Molecular dynamics investigations were performed to study thermal oxidation of single-crystal and polycrystalline Al–Mg alloys with low Mg content of up to 2.5 at. %. Structure, topological atom network and surface topography of the oxide films grown on Al–Mg surfaces at 300, 475 and 663 K are determined. Mg-content and temperature dependent oxide films developed on Al-Mg alloy substrates with two-phase oxide film formation as also confirmed experimentally. It is related with a gradual long-range order formation above 475 K for (Al,Mg)-oxide films, for which solid amorphous phase predominates over crystalline phase. The 1.12-nm-thick oxide films grown at 300 K are fully amorphous and build up from (Al, Mg)-oxide which the Al2O3 dominates. Increase of Mg coefficient confirms faster Mg diffusion to oxide/alloy interface at high oxidation temperature and the formation of MgO-like network. The presence of planar crystal defect (grain boundary, GB) into Al-Mg alloy substrate governs the kinetics of oxide film growth and its structure evolution. GB also compensate internal stresses during oxide film growth. Obtained results are in good agreement with experimental observations.

Investigation of biomolecular dynamics by sensitivity-enhanced 1H–2H CPMAS NMR using matrix-free dynamic nuclear polarization

Molecular dynamics of functional groups contain valuable information about structural properties and functional activities in biomolecules. NMR spectroscopy is a sensitive tool for the investigation of molecular dynamics over a wide range of timescales and thus may deepen the understanding of the biomolecules of interest. Here, we present an approach to use DNP-enhanced 2H NMR to study dynamics of selectively deuterated methyl groups in insoluble proteins such as amyloid beta (Aβ) fibrils. We adopted and optimized the matrix-free DNP approach by varying the amount of added polarizing agent as well as the rehydration level of model proteins. We show that the DNP enhancement obtained in 1H–2H cross-polarization (CP) MAS spectra may increase the sensitivity for selectively deuterated Aβ fibril samples by more than one order of magnitude, accelerating the collection of spin-lattice relaxation data in the DNP-accessible temperature range between 100 and 150 K by up to 400-fold. However, below the coalescence temperature, which describes the transition from the fast to the slow exchange regime, the experimentally obtained relaxation time constants suffer from a paramagnetic relaxation enhancement effect due to the presence of the polarizing agent. This seems to be a general effect for biomolecules as it is also confirmed for two other protein model systems. Our demonstration opens the possibility to extend the scope of 2H NMR for dynamics measurements to effective concentrations and/or temperatures below what is currently accessible; however, the observed interplay between paramagnetic relaxation and molecular dynamics also emphasizes the necessity for a better understanding of relaxation effects in DNP-enhanced NMR.

Force Fields, Quantum-Mechanical- and Molecular-Dynamics-Based Descriptors of Radiometal-Chelator Complexes.

Radiopharmaceuticals are currently a key tool in cancer diagnosis and therapy. Metal-based radiopharmaceuticals are characterized by a radiometal-chelator moiety linked to a bio-vector that binds the biological target (e.g., a protein overexpressed in a particular tumor). The right match between radiometal and chelator influences the stability of the complex and the drug's efficacy. Therefore, the coupling of the radioactive element to the correct chelator requires consideration of several features of the radiometal, such as its oxidation state, ionic radius, and coordination geometry. In this work, we systematically investigated about 120 radiometal-chelator complexes taken from the Cambridge Structural Database. We considered 25 radiometals and about 30 chelators, featuring both cyclic and acyclic geometries. We used quantum mechanics methods at the density functional theoretical level to generate the general AMBER force field parameters and to perform 1 µs-long all-atom molecular dynamics simulations in explicit water solution. From these calculations, we extracted several key molecular descriptors accounting for both electronic- and dynamical-based properties. The whole workflow was carefully validated, and selected test-cases were investigated in detail. Molecular descriptors and force field parameters for the complexes considered in this study are made freely available, thus enabling their use in predictive models, molecular modelling, and molecular dynamics investigations of the interaction of compounds with macromolecular targets. Our work provides new insights in understanding the properties of radiometal-chelator complexes, with a direct impact for rational drug design of this important class of drugs.

Molecular dynamics investigation of rotation-assisted grinding process for GaN with layered heterostructure of the Wurtzite/Zinc-blende

Molecular dynamics investigation of rotation-assisted grinding process for GaN with layered heterostructure of the Wurtzite/Zinc-blende