Molecular Dynamics Method Research Articles

The Fate of the Formic Acid Proton on the Anatase TiO2(101) Surface

As a prototype adsorption reaction of gas Brønsted acid on oxides, we study the adsorption of formic acid on anatase. We perform infrared spectroscopy measurements of adsorbed HCOOH and HCOOD on TiO2 nanopowders, from 13 K up to room temperature in an ultra‐high vacuum chamber. We assign the IR signals via computed spectra from nuclear quantum dynamics simulations using our divide‐and‐conquer semiclassical ab initio molecular dynamics method. The acid proton forms an extraordinarily short and strong hydrogen bond with the surface oxygen. The strength of this hydrogen bond, that compares to H bonds in ice at high pressures, is at the root of a substantial redshift with respect to the typical free OH stretching frequency, which eludes its straightforward detection.

Identification of potential dipeptidyl peptidase IV inhibitors from the ConMedNP library by virtual screening, and molecular dynamics methods

In this study, we screened novel dipeptidyl peptidase IV (DPP4) inhibitors from the ConMedNP library consisting of 3507 molecules. Interestingly, molecular docking, ADMET, and the anti-diabetic activity predictions suggest that three molecules, namely OTH_UD_XX06_1, GB19, and BMC_000104, have a high binding affinity toward DPP4. The molecular dynamics (MD) simulation results suggest that these hit molecules have a stable binding pose and occupy the binding pockets throughout the 200 ns simulation. The presence of intermolecular H-bonding between the ligands and DPP4 was observed throughout the simulation period. Thus, docking and MD results, predicted that the three compounds were the most potent DPP4 inhibitors that could putatively bind to the DPP4 active site via both conventional H-bonding and hydrophobic interactions. These results could aid the discovery of new drugs to treat type 2 diabetes.

First-principles study on the microstructure, band structure, mechanical and optical properties of AB-stacked bilayer graphene under constant neutron irradiation with different electric field magnitudes and directions

Carbon-based devices have superior performance and lower power consumption compared to silicon-based devices. However, graphene and related two-dimensional materials are easily influenced by radiation due to their extremely high surface-to-volume ratio. Under constant neutron irradiation conditions, there have been no studies on the effects of the magnitude and direction of an external electric field on various properties of the AB system. This study systematically investigated the neutron irradiation effects on the AB system and the influence of the different electric fields on the properties of the AB system under constant irradiation conditions using the density functional theory and ab initio molecular dynamics method that assigns energy to the primary knock-on atom. The results indicate that under constant neutron irradiation with different electric fields, the changes in system configuration dominate the influence on band structure, while the impact of surface ripples is relatively limited. Reducing the interlayer spacing of the system can make the configuration more stable, which makes the band structure under the electric field more stable. The primary factors influencing the Young's modulus (Y) of the system are changes in the microstructure and the appearance of surface ripples, while the influence of system configuration is relatively limited. Under the irradiation conditions, the electric field can to some extent accurately modulate the band gap of the system. However, it will also correspondingly reduce the system's Y to a certain extent, causing negative impacts on the electrical and thermal conductivity.

Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.

Binding thermodynamics and kinetics play critical roles in drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics of small molecules and flexible peptides using conventional molecular dynamics (cMD), due to limited simulation time scales. Based on our previously developed ligand Gaussian accelerated molecular dynamics (LiGaMD) method, we present a new approach, termed "LiGaMD3″, in which we introduce triple boosts into three individual energy terms that play important roles in small-molecule/peptide dissociation, rebinding, and system conformational changes to improve the sampling efficiency of small-molecule/peptide interactions with target proteins. To validate the performance of LiGaMD3, MDM2 bound by a small molecule (Nutlin 3) and two highly flexible peptides (PMI and P53) were chosen as the model systems. LiGaMD3 could efficiently capture repetitive small-molecule/peptide dissociation and binding events within 2 μs simulations. The predicted binding kinetic constant rates and free energies from LiGaMD3 were in agreement with the available experimental values and previous simulation results. Therefore, LiGaMD3 provides a more general and efficient approach to capture dissociation and binding of both small-molecule ligands and flexible peptides, allowing for accurate prediction of their binding thermodynamics and kinetics.

Exciton Transport in the Nonfullerene Acceptor O-IDTBR from Nonadiabatic Molecular Dynamics.

Theory, computation, and experiment have given strong evidence that charge carriers in organic molecular crystals form partially delocalized quantum objects that diffuse very efficiently via a mechanism termed transient delocalization. It is currently unclear how prevalent this mechanism is for exciton transport. Here we carry out simulation of singlet Frenkel excitons (FE) in a molecular organic semiconductor that belongs to the class of nonfullerene acceptors, O-IDTBR, using the recently introduced FE surface hopping nonadiabatic molecular dynamics method. We find that FE are, on average, localized on a single molecule in the crystal due to sizable reorganization energy and moderate excitonic couplings. Yet, our simulations suggest that the diffusion mechanism is more complex than simple local hopping; in addition to hopping, we observe frequent transient delocalization events where the exciton wave function expands over 10 or more molecules for a short period of time in response to thermal excitations within the excitonic band, followed by de-excitation and contraction onto a single molecule. The transient delocalization events lead to an increase in the diffusion constant by a factor of 3-4, depending on the crystallographic direction as compared to the situation where only local hopping events are considered. Intriguingly, O-IDTBR appears to be a moderately anisotropic 3D "conductor" for excitons but a highly anisotropic 2D conductor for electrons. Taken together with previous simulation results, two trends seem to emerge for molecular organic crystals: excitons tend to be more localized and slower than charge carriers due to higher internal reorganization energy, while exciton transport tends to be more isotropic than charge transport due to the weaker distance dependence of excitonic versus electronic coupling.

Dynamics of oil–CO2–water three-phase under the nanopore confinement effect: Implications for CO2 enhanced shale oil recovery and carbon storage

The widespread nanopores, diverse minerals, and varying water saturation in shale reservoirs complicate the mechanism analysis and performance prediction of CO2 enhanced oil recovery (CO2-EOR) and CO2 storage (CS) in hydrated nanopores. Therefore, molecular dynamics methods were used to simulate the process of CO2 replacing shale oil in hydrated nanopores of inorganic, organic and composite minerals. Importantly, the effects of mineral type, temperature, pressure and water content on CO2-EOR and CS performances in hydrated nanopores were analyzed, and the CO2-EOR mechanisms of dissolution, extraction, viscosity reduction, miscibility and competitive adsorption were revealed. The results show that water in illite, kerogen, and composite nanopores are distributed in the forms of water films, water clusters (films), and water columns, respectively. The replacement efficiency of shale oil in three types of nanopores is improved with increased water content but reduced in kerogen nanopores under high water content. Water is not conducive to the diffusion and viscosity reduction of oil in nanopores, but the miscibility and competitive adsorption of CO2 and oil are improved. The replacement efficiency is positively correlated with temperature and pressure. The increasing temperature promotes diffusion and viscosity reduction of oil and competitive adsorption between CO2 and oil in hydrated nanopores, and increasing pressure promotes miscibility and competitive adsorption. Water columns in kerogen and composite nanopores reduce the CS performance, while thin water films in illite nanopores improve it. Moreover, an excellent CS rate can be achieved at high temperatures and pressures, but the high temperature is not conducive to CS stability. This study provides a theoretical basis for CO2 injection to improve oil production and carbon storage performance in hydrated shale reservoirs and contributes to the optimization of CO2 injection schemes.

A molecular dynamics study on pore structure: Performance comparison between metal foam and artificial mesh porous surface

With the development of surface engineering, porous surfaces have emerged as a significant research subject in boiling heat transfer. The latter, in turn, plays a crucial role in various industries such as power plants, distillation plants, and microelectronic technology. In this paper, the Molecular Dynamics method is adopted to investigate the wicking dynamics and boiling dynamics of two porous surfaces: foam, which exhibits randomly distributed pores, and mesh, composed of ordered square wires with relatively uniform pore sizes. Three wettability, namely hydrophilic, neutral, and hydrophobic wetting states, are assigned to the two porous surfaces de-coupling the effect of wettability from surface structure. Results reveal that, during the wicking process, the foam surface shows better wetting ability as it absorbs liquid under both hydrophilic and neutral wettability. Comparatively, the mesh surface has the fastest wicking speed under hydrophilic wettability yet it becomes non-wetting under neutral wettability. During the boiling process, the boiling dynamics differ greatly under three wettability. More importantly, the difference in surface structure makes the foam surface possess a better heat transfer whereas the mesh surface causes gentle pressure variation. Our findings provide insights into the design of artificial porous surfaces for certain purpose and their potential application.

Differential study on the thermal–physical properties of metal and its oxide nanoparticle-formed nanofluids: Molecular dynamics simulation investigation of argon-based nanofluids

Abstract The influence of nanoparticle shape, volume fraction, and temperature on the thermal properties of nanofluids plays a pivotal role in engineering applications. However, there remains a considerable lack of systematic research comprehensively considering these factors to study the similarities and differences in the thermal properties of nanofluids composed of metals and their oxides and to conduct in-depth analyses of their internal mechanisms and characteristics. In this study, molecular dynamics simulations were conducted, employing reversing perturbation non-equilibrium molecular dynamics and non-equilibrium molecular dynamics methods. The thermal conductivity and viscosity of Al–Ar and Al2O3–Ar nanofluids were thoroughly investigated under the various influencing factors. Results reveal that under identical conditions, the thermal conductivity of Al–Ar nanofluid surpasses that of Al2O3–Ar nanofluid, exemplified by values such as 0.1832 W/m K (Al–Ar, 1.5%, cylinder, 86 K) versus 0.17745 W/m K (Al2O3–Ar, 1.5%, cylinder, 86 K). Furthermore, the viscosity of Al–Ar nanofluid is lower than that of Al2O3–Ar nanofluid, demonstrated by values such as 0.0004882 Pa S (Al–Ar nanofluid, 86 K, 2.5%, platelets) compared to 0.008975 Pa S (Al2O3–Ar nanofluid, 86 K, 2.5%, platelets). Subsequently, this study analyzed the difference in thermal conductivity between the two nanofluids from the perspective of microscale interface heat conduction by comparing the phonon density of states curves of Al, Ar, and Al2O3 in the two nanofluids for overlap. Subsequently, through radial distribution function analysis, the viscosity difference between Al–Ar and Al2O3–Ar nanofluids is explained based on nanofluid–solid interface and microstructural considerations. This research addresses the comprehensive lack of comparative studies on the thermal properties of nanofluids formed by metals and their oxides. The internal mechanisms underlying the thermal property differences of nanofluids formed by metals and their oxides were revealed from a microscopic perspective, which holds significant implications for the engineering applications of nanofluids.

Molecular dynamics study on tribological properties of AlCrFeCoNi HEA at different temperatures

The microscopically wear mechanism of AlCrFeCoNi HEA effected by high temperatures still remains unclear. In this work, the tribological properties of AlCrFeCoNi HEA and tungsten carbide (WC) at temperatures ranging from 250, 400, 550, 700, 850 °C was investigated using molecular dynamics methods. Additionally, the shear strain, contact stress, and energy change at different temperatures were analyzed to explore the atomic wear mechanism. The simulated results indicated that the coefficient of friction and wear rate decrease with the increasing temperature, since the dislocation types decrease and the kinetic energy and total system energy increase. And high temperature can inhibit the synergistic effect of strain accumulation and atomic wear on the surface of AlCrFeCoNi HEAs.

Molecular dynamics study on hydration characteristics of expansive clay minerals by temperature and inorganic salts

Most strata rock minerals have hydrophilic characteristics and the mineral surface is negatively charged. It can adsorb water molecules to form hydration layers on the mineral surface. The existence of hydration layer will reduce the effective pore diameter of rock pore microchannel. Thus, the development efficiency of crude oil is affected. Hydration layer compared to free water, water molecules are arranged in a highly ordered manner, with higher density and more stable toughness. Therefore, it is very important to study the structure of hydration layer adsorbed on rock wall and its influencing factors. Four different rock and mineral types are selected in this paper: Na-montmorillonite, quartz, kaolinite, calcite. Molecular dynamics method was used to simulate different temperature conditions and adding different inorganic salts. Study the influence of temperature and inorganic salts on the hydration layer structure of rock wall. The simulation results show that the increase of temperature and the addition of inorganic salts of different components have a great influence on the adsorption of water molecules on the rock wall, and it changes the original structure of the hydration layer. The adsorption of water molecules on different rock surfaces and the effect of different rock walls on the adsorption of hydration layer are described in molecular form. This study explains the mechanism of temperature and inorganic salts inhibiting water molecules from a microscopic perspective. It is of great significance to study the physical properties of hydration layer. It provides a theoretical basis for the field well wall stability research.

Implementation of Nonadiabatic Molecular Dynamics for Intersystem Crossing Based on a Time-Dependent Density-Functional Tight-Binding Method.

Intersystem crossing (ISC) and internal conversion (IC) are types of nonadiabatic transitions that play important roles in a wide range of fields, including photochemistry, photophysics, and photobiology. The nonadiabatic molecular dynamics (NA-MD) method is a powerful tool for computational simulations of dynamic phenomena involving nonadiabatic transitions. In this study, we implemented the NA-MD method, which treats ISC and IC on an equal footing, where the electronic structure is treated at the level of the time-dependent (TD) density-functional tight-binding (DFTB) method, a low-cost semiempirical analog of TD density functional theory (DFT). In particular, the spin-orbit coupling calculation algorithm was implemented in the TD-DFTB framework, and the results showed trends similar to those obtained using TD-DFT. In addition, the NA-MD method successfully reproduced ultrafast ISC of 2-nitronaphthalene.

Phonon-assisted charge carriers thermalization in semiconductor Si and metallic silicide NiSi2, CoSi2: A non-adiabatic molecular dynamics study

Recently, the cold source field-effect transistor (CSFET) has emerged as a promising solution to overcome Boltzmann tyranny in its ballistic regime, offering a steep-slope subthreshold swing (SS) of less than 60 mV/decade. However, challenges arise due to scattering, particularly from inelastic scattering, which can lead to significant degradation in SS through cold carrier thermalization. In this study, we delve into the theoretical investigation of the electronic excitation/relaxation dynamic process using the state-of-the-art nonadiabatic molecular dynamics (NAMD) method. The mixed quantum-classical NAMD proves to be a powerful tool for comprehensively analyzing cold carrier thermalization and transfer processes in semiconductor Si, as well as metallic silicides (NiSi2 and CoSi2). The approach of mixed quantum-classical NAMD takes into account both carrier decoherence and detailed balance, enabling the calculation of thermalization factors, relaxation times, scattering times, and scattering rates at various energy levels. The thermalization of carriers exhibits a gradual increase from low to high energy levels. Achieving partial thermalization from the ground state to reach the thermionic current window occurs within a sub-100 fs time scale. Full thermalization across the entire energy spectrum depends sensitively on the barrier height, with the scattering rate exponentially decreasing as the energy of the out-scattering state increases. Notably, the scattering rate of NiSi2 and CoSi2 is two orders of magnitude higher than that of Si, attributed to their higher density of states compared to Si. This study not only provides insights into material design for low-power tunnel field-effect transistors but also contributes valuable information for advancing CSFET in emerging technologies.

Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.

Because most proteins have buried active sites, protein tunnels or channels play a crucial role in the transport of small molecules into buried cavities for enzymatic catalysis. Tunnels can critically modulate the biological process of protein-ligand recognition. Various molecular dynamics methods have been developed for exploring and exploiting the protein-ligand conformational space to extract high-resolution details of the binding processes, a recent example being energetically unbiased high-throughput adaptive sampling simulations. The current study systematically contrasted the role of integrating prior knowledge while generating useful initial protein-ligand configurations, called seeds, for these simulations. Using a nontrivial system of a haloalkane dehalogenase mutant with multiple transport tunnels leading to a deeply buried active site, simulations were employed to derive kinetic models describing the process of association and dissociation of the substrate molecule. The most knowledge-based seed generation enabled high-throughput simulations that could more consistently capture the entire transport process, explore the complex network of transport tunnels, and predict equilibrium dissociation constants, koff/kon, on the same order of magnitude as experimental measurements. Overall, the infusion of more knowledge into the initial seeds of adaptive sampling simulations could render analyses of transport mechanisms in enzymes more consistent even for very complex biomolecular systems, thereby promoting drug development efforts and the rational design of enzymes with buried active sites.

Mechanism exploration of the modified asphalt binders with sustainable rapeseed-based derivatives using multi-scale evaluation method

Due to the concerns of sustainability, environment, and economy that are associated with non-renewable petroleum-based additives, there has been a growing interest in bio-additives derived from renewable feedstocks. This study aims to reveal the modification mechanism of three bio-additives derived from rapeseed on the base asphalt. The exploration of modification mechanism helped to explain the distinct rheological properties of bio-modified asphalt binders presented in a previous study. The effect of three bio-additives on the surface morphology, micro-mechanical properties, adhesivity, and chemical structure of base asphalt binders were investigated via Atomic Force Microscopy (AFM) and Fourier Transform Infrared spectrometer (FTIR) tests. The Electrostatic potential distribution and the orbital energy was analyzed via density functional theory (DFT) calculation to explore the inherit polarity of both the three bio-additives and asphalt components. Furthermore, molecular dynamic (MD) methods were used to evaluate the compatibility mechanism and aggregation tendency of asphalt components and bio-additives. The results showed that the electrostatic potential and the orbital energy of three bio-additives predominantly centered around the polar group. Specifically, AERO exhibited highest electrostatic potential distribution and lowest energy gap, indicating its heightened polarity. Moreover, the solution parameter difference value of bio-modified asphalt fell within 0.2 (J/m3)0.5, indicating great compatibility between asphalt and bio-additives, especially for ERO. Additionally, three bio-additives mitigated the aggregation of asphaltene within the asphalt due to their electrostatic interaction, especially notable in the cases of ERO and AERO. Furthermore, a cross-link network was formed within AERO-modified asphalt binders owing to its heightened polarity, fostering hydrogen bonding interactions internally and promoting the aggregation of saturate and resin factions around it. Consequently, this led to enhanced modulus and elasticity in the AERO-modified asphalt binders. Rapeseed derivatives as asphalt additives would be a sustainable and durable material for pavement construction and maintenance. It provides a theoretical basis for advancing the practical application of renewable vegetable oils in road engineering, which has exceptional economic and social benefits.

Discovery of a novel homocysteine thiolactone hydrolase and the catalytic activity of its natural variants.

Homocysteine thiolactone (HTL), a toxic metabolite of homocysteine (Hcy) in hyperhomocysteinemia (HHcy), is known to modify protein structure and function, leading to protein damage through formation of N-Hcy-protein. HTL has been highly linked to HHcy-associated cardiovascular and neurodegenerative diseases. The protective role of HTL hydrolases against HTL-associated vascular toxicity and neurotoxicity have been reported. Although several endogeneous enzymes capable of hydrolyzing HTL have been identified, the primary enzyme responsible for its metabolism remains unclear. In this study, three human carboxylesterases were screened to explore new HTL hydrolase and human carboxylesterase 1 (hCES1) demonstrates the highest catalytic activity against HTL. Given the abundance of hCES1 in the liver and the clinical significance of its single-nucleotide polymorphisms (SNPs), six common hCES1 nonsynonymous coding SNP (nsSNPs) variants were examined and characterized for their kinetic parameters. Variants E220G and G143E displayed 7.3-fold and 13.2-fold lower catalytic activities than its wild-type counterpart. In addition, the detailed catalytic mechanism of hCES1 for HTL hydrolysis was computational investigated and elucidated by Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) method. The function of residues E220 and G143 in sustaining its hydrolytic activity of hCES1 was analyzed, and the calculated energy difference aligns well with experimental-derived results, supporting the validity of our computational insights. These findings provide insights into the potential protective role of hCES1 against HTL-associated toxicity, and warrant future studies on the possible association between specific genetic variants of hCES1 with impaired catalytic function and clinical susceptibility of HTL-associated cardiovascular and neurodegenerative diseases.

Molecular dynamics simulation on crystal morphology of NH4ClO4.

Ammonium perchlorate (NH4ClO4, abbreviated as AP) has the advantages of high oxygen content, high density, and good compatibility, and has significant application prospects in the field of energetic materials. The crystal morphology has a great influence on the properties and sensibility of energetic materials, and a single experimental means is difficult in exploring the crystals; therefore, the crystal morphology of AP is investigated using molecular dynamics simulation complemented with experiments, to theoretically analyze the differences in AP crystal habit and the interactions between solvent molecules and the main growing crystal surfaces of AP. The results show that AP crystal is mainly composed of five independent crystal surfaces (0 0 1), (0 1 0), (1 0 0), (1 0 1), and (1 0 -1) in vacuum using the BFDH laws, with (0 0 1) surface being the main growth crystal surface. In contrast, in H2O solvent, the (1 0 1) and (1 0 -1) surfaces disappear, and the AP mainly consists of (0 0 1), (0 1 0), and (1 0 0) surfaces with a rectangular shape. The crystal morphology obtained from theoretical prediction is in good agreement with that obtained from experimental culture. This paper can provide a new idea for the cultivation and preparation of AP large crystals, and promote the application of AP crystals in energetic materials. The crystal morphologies of AP in vacuum and H2O solvent under Dreiding force field were predicted based on attachment energy model by using molecular dynamics method in Materials Studio 2019 software. The entire molecular dynamics simulation was carried out under the NTV system, the temperature control method was selected as Anderson, and the system temperature was set to 298 K. The simulation time was set to 40 ps, the step size was set to 1 fs, and the data were outputted every 5000 steps.

Molecular dynamics study on the thermal properties of DGEBA/DETA/Ag/SWCNT-Ag composite materials.

Traditional conductive adhesives based on epoxy resin system often encounter problems such as high brittleness and low heat resistance. Therefore, it is particularly important to improve the thermal and mechanical properties of the conductive adhesive. In this study, the effects of SWCNT-Ag and SWCNT fillers on the thermal properties of DGEBA/DETA/Ag conductive adhesive system were studied by using molecular dynamics to construct different cross-linking models. The final results show that the addition of SWCNT and SWCNT-Ag can significantly improve the thermal properties of the conductive adhesive. However, the nanosilver particles on the surface of SWCNT-Ag act as a bridge for the connection between SWCNT and Ag in the conductive adhesive. Therefore, SWCNT-Ag has a more positive impact on the thermal properties of DGEBA/DETA/Ag conductive adhesive system. In this paper, the influence of SWCNT-Ag on the thermal properties of traditional DGEBA/DETA/Ag conductive adhesive system was studied by using Materials Studio software. The volume shrinkage, glass transition temperature, thermal expansion coefficient, and thermal conductivity of the material were calculated based on COMPASS force field. The thermal conductivity is calculated by using reverse non-equilibrium molecular dynamics method. Finally, it is found that SWCNT-Ag has a positive effect on the thermal properties of the conductive adhesive system by comparing several groups of calculation data.

Modeling collisional kinetic energy damping, heating, and cooling of ions in mass spectrometers: A tutorial perspective

Many powerful methods in mass spectrometry rely on activation of ions by high-energy collisions with gas particles. For example, multiple Collision Induced Dissociation (CID) has been used for many years to determine structural information for ions ranging from small organics to large, native-like protein complexes. More recently, Collision Induced Unfolding (CIU) has proved to be a very powerful method for understanding high-order protein structure and detecting differences between similar proteins. Quantifying the thermochemistry underlying dissociation/unfolding in these experiments can be quite challenging without reliable models of ion heating and cooling. Established physical models of CID are valuable in predicting ion heating but do not explicitly include mechanisms for cooling, which may play a large part in CID/CIU in modern instruments. Ab initio and Molecular Dynamics methods are extremely computationally expensive for modeling CID/CIU of large analytes such as biomolecular ions. In this tutorial perspective, limiting behaviors of ion kinetic energy damping, heating, and cooling set by “extreme” cases are explored, and an Improved Impulsive Collision Theory and associated software (“Ion Simulations of the Physics of Activation”, IonSPA) are introduced that can model all of these for partially inelastic collisions. Finally, examples of modeled collisional activation of native-like protein ions under realistic experimental conditions are discussed, with an outlook toward the use of IonSPA in accessing the thermochemical information hidden in CID breakdown curves and CIU fingerprints.

Synthesis, Docking, and Machine Learning Studies of Some Novel Quinolinesulfonamides-Triazole Hybrids with Anticancer Activity.

In the presented work, a series of 22 hybrids of 8-quinolinesulfonamide and 1,4-disubstituted triazole with antiproliferative activity were designed and synthesised. The title compounds were designed using molecular modelling techniques. For this purpose, machine-learning, molecular docking, and molecular dynamics methods were used. Calculations of the pharmacokinetic parameters (connected with absorption, distribution, metabolism, excretion, and toxicity) of the hybrids were also performed. The new compounds were synthesised via a copper-catalysed azide-alkyne cycloaddition reaction (CuAAC). 8-N-Methyl-N-{[1-(7-chloroquinolin-4-yl)-1H-1,2,3-triazol-4-yl]methyl}quinolinesulfonamide was identified in in silico studies as a potential strong inhibitor of Rho-associated protein kinase and as a compound that has an appropriate pharmacokinetic profile. The results obtained from in vitro experiments confirm the cytotoxicity of derivative 9b in four selected cancer cell lines and the lack of cytotoxicity of this derivative towards normal cells. The results obtained from silico and in vitro experiments indicate that the introduction of another quinolinyl fragment into the inhibitor molecule may have a significant impact on increasing the level of cytotoxicity toward cancer cells and indicate a further direction for future research in order to find new substances suitable for clinical applications in cancer treatment.

Complex Fluid Models of Mixed Quantum–Classical Dynamics

Several methods in nonadiabatic molecular dynamics are based on Madelung’s hydrodynamic description of nuclear motion, while the electronic component is treated as a finite-dimensional quantum system. In this context, the quantum potential leads to severe computational challenges and one often seeks to neglect its contribution, thereby approximating nuclear motion as classical. The resulting model couples classical hydrodynamics for the nuclei to the quantum motion of the electronic component, leading to the structure of a complex fluid system. This type of mixed quantum–classical fluid models has also appeared in solvation dynamics to describe the coupling between liquid solvents and the quantum solute molecule. While these approaches represent a promising direction, their mathematical structure requires a certain care. In some cases, challenging higher-order gradients make these equations hardly tractable. In other cases, these models are based on phase-space formulations that suffer from well-known consistency issues. Here, we present a new complex fluid system that resolves these difficulties. Unlike common approaches, the current system is obtained by applying the fluid closure at the level of the action principle of the original phase-space model. As a result, the system inherits a Hamiltonian structure and retains energy/momentum balance. After discussing some of its structural properties and dynamical invariants, we illustrate the model in the case of pure-dephasing dynamics. We conclude by presenting some invariant planar models.