Structural Molecular Dynamics Research Articles

Accelerating Molecular Dynamics Simulations Using Socket-Based Interprocess Communication.

Molecular dynamics (MD) simulations are essential for studying the time evolution of molecular systems. Still, their efficiency is often bottlenecked by file-based interprocess communication (IPC) between MD and electronic structure programs. We present a socket-based IPC implementation that dramatically accelerates MD simulations, reducing the computational time by >10-fold compared to those of traditional file-based methods. Our approach, applied to nonadiabatic molecular dynamics with the Newton-X program, eliminates disk read/write overhead, allowing for faster simulations over longer time scales. This method opens the door to more efficient high-throughput simulations, providing new opportunities for exploring complex molecular processes in real time.

Influence of Pnictogen and Ligand Framework on the Lewis Acidity and Steric Environment in Pnictogen Pincer Complexes.

Pnictogen pincer complexes are a fascinating class of compounds due to their dynamic molecular and electronic structures, and valuable stoichiometric or catalytic reactivity. As recognition of their unique chemistry has grown, so too has the library of pincer ligands employed and pnictogen centres engaged to prepare them. Here we computationally study how the choice of pincer ligand framework and pnictogen influence the electronic and steric outcomes within the complexes obtained. The most relevant electronic parameter is the pnictogen-centred electrophilicity, which has been quantified by fluoride ion affinities and LUMO energies, while the most relevant steric parameter is the crowding around the central pnictogen, which has been quantified by the %Vbur values and visualized using steric maps. The resulting trends are analyzed with reference to binding pocket size, acceptor orbital type, electronic delocalization, π-donor strengths, and heteroatom incorporation. Thus, considering 16 ligand frameworks and 4 heavy pnictogen centres, this study provides a broad-spectrum view of stereo-electronic variation in pnictogen pincer complexes, which, together with a recent study on geometric variation in the same family, provides a substantial dataset to guide future molecular design and reactivity studies.

Development of Multiscale Force Field for Actinide (An3+) Solutions.

A multiscale force field (FF) is developed for an aqueous solution of trivalent actinide cations An3+ (An = U, Np, Pu, Am, Cm, Bk, and Cf) by using a 12-6-4 Lennard-Jones type potential considering ion-induced dipole interaction. Potential parameters are rigorously and automatically optimized by the meta-multilinear interpolation parametrization (meta-MIP) algorithm via matching the experimental properties, including ion-oxygen distance (IOD) and coordination number (CN) in the first solvation shell and hydration free energy (HFE). The water solvent models incorporate an especially developed polar coarse-grained (CG) water scheme named PW32 and three widely used all-atom (AA) level SPC/E, TIP3P, and TIP4P water schemes. Each PW32 is modeled as two bonded beads to represent three neighboring water molecules, the simulation efficiency of which is 1 to 2 orders of magnitude higher than that of AA waters. The newly developed FF shows high accuracy and transferability in reproducing the IOD, CN, and HFE of An3+. The molecular structure and water exchange dynamics of the first An3+ hydration shell and the ionic (van der Waals) radii are reinvestigated in this work. Moreover, the new FF can readily be transferred to other popular FFs, as it has practicably predicted the permeability of An3+ in a graphene oxide filter within the framework of optimized potentials for liquid simulations (OPLS)-AA FF. It holds promise for applications in exploring actinide aqueous solutions with multiscale computational overhead.

Toward On-Demand Polymorphic Transitions of Organic Crystals via Side Chain and Lattice Dynamics Engineering.

Controlling polymorphism, namely, the occurrence of multiple crystal forms for a given compound, is still an open technological challenge that needs to be addressed for the reliable manufacturing of crystalline functional materials. Here, we devised a series of 13 organic crystals engineered to embody molecular fragments undergoing specific nanoscale motion anticipated to drive cooperative order-disorder phase transitions. By combining polarized optical microscopy coupled with a heating/cooling stage, differential scanning calorimetry, X-ray diffraction, low-frequency Raman spectroscopy, and calculations (density functional theory and molecular dynamics), we proved the occurrence of cooperative transitions in all the crystalline systems, and we demonstrated how both the molecular structure and lattice dynamics play crucial roles in these peculiar solid-to-solid transformations. These results introduce an efficient strategy to design polymorphic molecular crystalline materials endowed with specific molecular-scale lattice and macroscopic dynamics.

Integrated computational characterization of valosin-containing protein double-psi β-barrel domain: Insights into structural stability, binding mechanisms, and evolutionary significance.

Valosin-containing protein (VCP) plays a crucial role in various cellular processes, yet the molecular mechanisms and structural dynamics of its double-psi β-barrel (DPBB) domain, particularly in human, remain insufficiently explored. While previous studies have characterized the VCP_DPBB domain in other organisms, such as thermoplasma acidophilum and methanopyrus kandleri, its evolutionary conservation, binding potential, and stability in human require further investigation. To address this gap, we first employed all-atom molecular dynamics (AAMD) simulations to examine the structural dynamics of the human VCP_DPBB domain. We also assessed its amino acid interaction energies, stability, folding enthalpy, evolutionary conservation, solubility, and crystallizability using various computational frameworks. Additionally, to uncover the plausible biological function, protein-peptide docking was performed to evaluate the interactions between the DPBB domain and the C-terminal gp78 peptide of the E3 ubiquitin ligase. Further, AAMD and coarse-grained molecular dynamics (CGMD) simulations explored the binding preferences, fluctuations, and stability of human VCP_DPBB-gp78 complexes. Our findings indicate that, while thermoplasma acidophilum VCP_DPBB-gp78 showed stronger initial binding, the human VCP_DPBB-gp78 complex exhibited superior stability, binding affinity, and more stabilizing interactions. This integrated analysis provides valuable insights into the evolutionary significance and functionality of the DPBB domain, with potential therapeutic implications for VCP-related diseases.

Binding of a Drug (Colchicine) to L-Asparaginase Enzyme Using Multispectroscopic, Thermodynamics, and Simulation Studies: Possible Implication in Acute Lymphoblastic Leukemia Treatment.

The research aims to elucidate how drug interactions affect the activity of L-asparaginase (L-ASNase), an essential enzyme in cancer treatment, especially for acute lymphoblastic leukemia (ALL). Understanding these interactions is crucial for optimizing treatment effectiveness and reducing adverse effects. This study explores the intricate molecular interactions and structural dynamics of L-ASNase upon binding with colchicine. Fluorescence quenching experiments were conducted at various temperatures (298, 303, and 310 K), revealing notable interactions between L-ASNase and colchicine. These interactions were characterized by a reduction in fluorescence intensity and a blue shift in emission maxima. Additional analyses, including the determination of Stern-Volmer quenching constants (KSV), bimolecular quenching rate constants (kq), and thermodynamic parameters, indicated a static quenching mechanism with moderate binding affinities (Ka: 1.40-2.71 × 104 M-1) across different temperatures. Thermodynamic study suggested positive enthalpy and entropy changes (ΔH° = -10.26 kcal mol-1; ΔS° = -14.19 cal mol-1 K-1), suggesting a spontaneous reaction with negative ΔG° values (-5.86 to -6.03 kcal mol-1). FRET measurements supported optimal distances (r and Ro) for FRET occurrence, reinforcing the static quenching mechanism. Molecular docking further supported these findings, revealing a 1:1 stoichiometric binding ratio for L-ASNase:colchicine and elucidating specific binding orientations and interactions critical for complex stability. Subsequent molecular dynamics simulations spanning 100 ns underscored the stability of the L-ASNase-colchicine complex, with minimal deviations observed in key structural parameters such as RMSD, RMSF, Rg, and SASA. Additionally, spectroscopic analyses, including circular dichroism (CD), synchronous fluorescence, and 3D fluorescence provided insights into the conformational changes and alterations in the microenvironment of aromatic amino acid residues in L-ASNase upon colchicine binding. Moreover, L-ASNase activity was slightly reduced by 25% in the presence of colchicine. This comprehensive investigation sheds light on the molecular intricacies of the L-ASNase-colchicine complex, advancing our understanding of drug-target interactions and offering potential avenues for therapeutic applications.

Understanding and simulating mechanochromism in dye-dispersed polymer blends: from atomistic insights to macroscopic properties.

In this work, we propose a computational protocol enabling the simulation of mechanochromic responses in dye-dispersed polymer blends. The main objective is the modeling of the molecular-level structural changes responsible for the modulation of the photophysical properties that lead to the mechanochromic phenomenon. In this demonstrative study, we focus on predicting the changes in optical absorption displayed by a model system consisting of a dimer of a tetraphenylethylene derivative dispersed in a polyethylene matrix. The blend is subjected to an external stimulus that causes a modulation of the polymer matrix density that translates, in turn, into the emergence of specific mechanical constraints on the optically active dimers. The accurate description of this phenomenon requires the reliable sampling of the dimer configurations induced by the interaction with the matrix under stress. These molecular geometries are associated with modified electronic structures that confer novel absorption responses to the dispersed dyes. In the present contribution, the sampling of these structures is achieved through classical molecular dynamics (MD) simulations including a model element to apply an anisotropic mechanical force. This element allows the microscopic modeling of the chains' and dyes' structural rearrangements under stress. After the sampling, we compare the results of two approaches for the prediction of the optical response: (i) the calculation of a mean response from a statistical average over quantum chemical calculations on the sampled MD structures and (ii) a prediction via a more expensive hybrid scheme allowing the relaxation of the sampled molecular geometries in the presence of the matrix constraints.

Characterizing the Orderliness of Interfacial Water through Stretching Vibrations.

Spatial orderliness, which is the orderly structure of molecules, differs significantly between interfacial water and bulk water. Understanding this property is essential for various applications in both natural and engineered environments. However, the subnanometer thickness of interfacial water presents challenges for direct and rapid characterization of its structural orderliness. Herein, through molecular dynamics simulations and infrared spectral analysis of interfacial water in a graphene slit pore, we reveal a hyperbolic tangent relationship between the water ordering and its O-H stretching information in the infrared spectrum. Specifically, O-H symmetric stretching dominated in the highly ordered water structure, while a transition to the asymmetric stretching corresponded to an increase in the degree of disorder. Thus, the O-H stretching behavior could serve as a useful and quick assessment of the orderliness of interfacial water. This work provided insights into interfacial water's unique molecular network and structural dynamics and identified the stretching vibrations' key role in its degree of order, providing insight for fields such as nanotechnology, biology, and material science.

Carbonyl stretching band in amides as Lorentz oscillator. Insights into anharmonicity and local environment in the liquid phase from NIR and MIR spectra of N-methylformamide and di-N,N-methylformamide

We investigated the anharmonicity and intermolecular interactions of N-methylformamide (NMF) and di-N,N-methylformamide (DMF) in the neat liquid phase with particular interest in the amide bands. The vibrational spectra, complex refractive index, and complex electric permittivity were determined in in the mid- (MIR) and near-infrared (NIR) regions (11,500–560 cm−1; 870–17857 nm). Dispersion analysis was based on the Classical Damped Harmonic Oscillator (CDHO) and simultaneous modelling of the real and imaginary components of the spectra. This data delivered insights into the vibrational energy dissipation and self-association in liquid amides. Identification of the MIR and NIR bands was based on anharmonic GVPT2//B3LYP/6-311++G(d,p) calculations. DMF and NMF follow distinct self-association, evidenced in the MIR fingerprint by the two components of the νCO, the analog of the Amide I band. These conclusions are supported by the structural information derived from the NIR spectra. Furthermore, the contribution of overtones and combination bands in the MIR spectra of amides was examined. The conclusions on molecular interactions and structural dynamics of NMF and DMF contribute to a deeper understanding of the effects of changes in the local environment of the amide group.

Molecular Structure and Rotational Dynamics in the Acetonitrile:Acetylene (1:2) Plastic Co-crystal at Titan Conditions

Molecular Structure and Rotational Dynamics in the Acetonitrile:Acetylene (1:2) Plastic Co-crystal at Titan Conditions

Hydration effects on molecular structure, vibrational, electronic properties, drug-likeness analysis, molecular docking, and molecular dynamics studies of (Z)-3-(2-oxo-2-phenylethylidene)indolin-2-one

This study examines how solvation models, including COSMO, CPCM, PCM, and SMD, affect the conformations, molecular structure, vibrational behaviors, and electronic properties of the (Z)-3-(2-oxo-2-phenylethylidene)indolin-2-one (Z3-2O2PEI) molecule within the framework of the B3LYP/cc-pVTZ model chemistry, along with its potential effectiveness as a drug for treating COVID-19. The most stable molecular conformation of the studied coùpound was identified in the presence of the COSMO solvent. The theoretical vibrational frequencies matched the experimentally observed FT-IR and Raman data. Solvent influences on the UV–vis spectra of Z3-2O2PEI revealed electronic transitions from n to π* and π to π* orbitals, along with evidence of intermolecular charge transfer (ICT) supported by analyses of Frontier Molecular Orbitals (FMO) and Natural Bond Orbitals (NBO). The examinations of Mulliken atomic charge distributions and molecular electrostatic potential surfaces reveal the electrophilic and nucleophilic sites of the molecule under study. Non-covalent Interaction (NCI) analysis confirmed the presence of steric effects and Van der Waals interactions within the compound. According to molecular docking studies, the Z3-2O2PEI molecule exhibits significant binding affinity for PLpro, a protein targeted in COVID-19 treatment. This finding is supported by subsequent molecular dynamics analysis, validating the docking results.

Molecular structure, spectroscopic (FT-IR, NMR and UV–Vis), electronic properties, molecular docking, and molecular dynamics studies on novel thiazolidinone derivative: A potent breast cancer drug

This study details the synthesis, characterization, and comprehensive computational analysis of a novel (R)-camphor-based thiazolidinone derivative. The structural integrity of the synthesized compound was confirmed using 1H- and 13CNMR spectroscopy as well as HRMS. Theoretical vibrational modes were successfully assigned and matched well with the observed FT-IR spectrum. Simulated NMR values were in excellent agreement with experimental chemical shifts, showing maximum deviations of less than 1.5 ppm for 1H and 4 ppm for 13C. UV–vis spectroscopy revealed n→π* and π→π* transitions in thiazolidinone, with intermolecular charge transfer (ICT) corroborated by Frontier Molecular Orbital (FMO), density of states (DOS), and Natural Bond Orbital (NBO) analyses. Molecular docking studies indicated that thiazolidinone exhibited strong inhibitory activity against the breast cancer target protein 6HQO, which was further validated by molecular dynamics simulations, confirming the stability and accuracy of the docking results.

Targeting MDM2-p53 interaction in Glioblastoma: Transcriptomic analysis and Peptide-Based inhibition strategy

MDM2 is a gene that encodes a protein involved in cell survival, growth, and DNA repair. It has been implicated in the development and progression of glioblastoma (GBM). Inhibition of the MDM2-p53 interaction has emerged as a promising strategy for treating GBM. In this study, we performed comprehensive transcriptomic expression analysis from diverse datasets and observed MDM2 overexpression in a subset of GBM cases. MDM2 negatively regulates the major onco-suppressor p53. The interaction between MDM2 and p53 is a promising target for cancer therapy, as it can trigger p53-mediated cell death in response to different stress conditions, such as oncogene activation or DNA damage. In this study, we have identified a peptide-based inhibition of MDM2 as a therapeutic strategy for GBM. We have further validated the stability of the MDM2-peptide interaction using a molecular structural dynamics approach. The major trajectories, including root mean square of deviation (RMSD), root mean square of fluctuation (RMSF), and radius of gyration (RoG), indicate that the candidate peptides have a more stable binding compared to the native ligand and control drug. The stability of the binding interaction was further estimated by MMGBSA analysis, which also suggests that MDM2 has a stable binding with both peptide molecules. Based on these results, peptides P-1843 and P-3837 could be tested further for experimental validation to confirm their targeted inhibition of MDM-2. This approach could provide a highly selective and efficient inhibitor with potentially fewer side effects and less toxicity compared to small drug-based molecules.

EMMAs: Implementation and Assessment of a Suite of Cross-Disciplinary, Case-Based High School Activities to Explore Three-Dimensional Molecular Structure, Noncovalent Interactions, and Molecular Dynamics.

Students frequently develop misconceptions about noncovalent interactions that make it challenging for them to appropriately interpret aspects of molecular structure and interactions critical to myriad applications. We hypothesized that computational molecular modeling and visualization could provide a valuable approach to help address these core misconceptions when students are first exposed to these concepts in secondary school chemistry courses. Here, we present a series of activities exploring biomolecular drug-target interactions using molecular visualization software and an introduction to molecular dynamics methods that were implemented in secondary school classrooms. A pre- and postsurvey approach that incorporated Likert response type, written free response, and drawing-based items demonstrated that students gained an enhanced conceptualization of intermolecular interactions, particularly related to aspects of shape complementarity, after completing the activities. Students also expressed increased comfort with and facility in utilizing different three-dimensional representations of molecules in their postsurvey responses. The activities led to an increased appreciation of interdisciplinary connections of chemistry with mathematics and physics. Overall, the modular activities presented provide a relatively time-efficient and accessible manner to help promote an understanding of a traditionally challenging topic for beginning chemistry students while introducing them to contemporary research tools.

M-Polynomial and NM-Polynomial Methods for Topological Indices of Polymers

Topological indices (TIs) are numerical tools widely applied in chemometrics, biomedicine, and bioinformatics for predicting diverse physicochemical attributes and biological activities within molecular structures. Despite their significance, the challenges in deriving TIs necessitate novel approaches. This study addresses the limitations of conventional methods in dealing with dynamic molecular structures, focusing on the neighborhood M-polynomial (NM-polynomial), a pivotal polynomial for calculating degree-based TIs. Current literature acknowledges these polynomials but overlooks their limited adaptability to intricate biopolymer relationships. Our research advances by computing degree-based and neighborhood degree-based indices for prominent biopolymers, including polysaccharides, poly-γ-glutamic acid, and poly-L-lysine. Through innovative utilization of the NM-polynomial and the M-polynomial, we establish a fresh perspective on molecular structure and topological indices. Moreover, we present diverse graph representations highlighting the nuanced correlations between indices and structural parameters. By systematically investigating these indices and their underlying polynomials, our work contributes to predictive modelling in various fields. This exploration sheds light on intricate biochemical systems, offering insights into applications encompassing medicine, the food industry, and wastewater treatment. This research deepens our understanding of complex molecular interactions and paves the way for enhanced applications in diverse industries.

An investigation of water status in gelatin methacrylate hydrogels by means of water relaxometry and differential scanning calorimetry.

The relationship between molecular structure and water dynamics is a fundamental yet often neglected subject in the field of hydrogels for drug delivery, bioprinting, as well as biomaterial science and tissue engineering & regenerative medicine (TE&RM). Water is a fundamental constituent of hydrogel systems and engages via hydrogen bonding with the macromolecular network. The methods and techniques to measure and reveal the phenomena and dynamics of water within hydrogels are still limited. In this work, differential scanning calorimetry (DSC) was used as a quantitative method to analyze freezable (including free and freezable bound) and non-freezable bound water within gelatin methacrylate (GelMA) hydrogels. Nuclear magnetic resonance (NMR) is a complementary method for the study of water behavior and can be used to measure the spin-relaxation of water hydrogen nuclei, which is related to water dynamics. In this research, nuclear magnetic resonance relaxometry was employed to investigate the molecular state of water in GelMA hydrogels using spin-lattice (T1) and spin-spin (T2) spin-relaxation time constants. The data displays a trend of increasing bound water content with increasing GelMA concentration. In addition, T2 values were further applied to calculate microviscosity and translational diffusion coefficients. Water relaxation under various chemical environments, including different media, temperatures, gelatin sources, as well as crosslinking effects, were also examined. These comprehensive physical data sets offer fundamental insight into biomolecule transport within the GelMA hydrogel system, which ultimately are important for drug delivery, bioprinting, as well as biomaterial science and TE&RM communities.

Molecular structural dynamics in water–ethanol mixtures: Spectroscopy with polarized neutrons simultaneously accessing collective and self-diffusion

Binary mixtures of water with lower alcohols display non-linear phase behaviors upon mixing, which are attributed to potential cluster formation at the molecular level. Unravelling such elusive structures requires investigation of hydrogen-bonding sub-nanosecond dynamics. We employ high-resolution neutron time-of-flight spectroscopy with polarization analysis in combination with selective deuteration to study the concentration-dependent structural dynamics in the water rich part of the phase diagram of water–ethanol mixtures. This method enables simultaneous access to atomic correlations in space and time and allows us to separate spatially incoherent scattering probing self-diffusion of the ethanol fraction from the coherent scattering probing collective diffusion of the water network as a whole. Our observations indicate an enhanced rigidity of the hydrogen bond network at the mesoscopic length scale compared to the molecular scale as the ethanol fraction increases, which is consistent with the hypothesis of clusters.

Structural Changes to the Gd‐DTPA Complex at Varying Ligand Protonation State

AbstractDiethylenetriaminepentaacetic acid (DTPA) is a chelating agent whose complex with the Gd3+ ion is used in medical imaging. DTPA is also used in lanthanide‐actinide separation processes. As protonation of the DTPA ligand can facilitate dissociation of the Gd3+ ion from the Gd‐DTPA complex, this work investigates the coordination structures of the aqueous Gd3+ ion and its environment when chelated by DTPA in eight different DTPA protonation states. Both classical and ab initio molecular dynamics (MD) simulations are conducted to model the solvated complexes. Extended X‐ray absorption fine structure (EXAFS) measurements of the Gd3+aqua ion, and the Gd‐DTPA complex at pH 1 and 11, are compared to EXAFS spectra predicted from the MD simulations to verify the accuracy of the MD structures. The findings of this work provide atomic‐level details into the fluctuating Gd‐DTPA complex environment as the DTPA ligand gradually detaches from the Gd3+ ion with increased protonation.

Application of molecular dynamic simulations in modeling the excited state behavior of confined molecules.

Relative to isotropic organic solvent medium, the structure and conformation of a reactant molecule in an organized and confining medium are often different. In addition, because of the rigidity of the immediate environment, the reacting molecule have a little freedom to undergo large changes even upon gaining energy or modifications in the electronic structure. These alterations give rise to differences in the photochemistry of a molecular and supramolecular species. In this study, one such example is presented. α-Alkyl dibenzylketones upon excitation in isotropic solvents give products via Norrish type I and type II reactions that are independent of the chain length of the alkyl substituent. On the other hand, when these molecules are enclosed within an organic capsule of volume ~ 550Å3, they give products that are strikingly dependent on the length of the α-alkyl substitution. These previously reported experimental observations are rationalized based on the structures generated by molecular modeling (docking and molecular dynamics (MD) simulations). It is shown that MD simulations that are utilized extensively in biologically important macromolecules can also be useful to understand the excited state behavior of reactive molecules that are part of supramolecular assemblies. These simulations can provide structural information of the reactant molecule and the surroundings complementing that with the one obtained from 1 and 2D NMR experiments. MD simulated structures of seven α-alkyl dibenzylketones encapsulated within the octa acid capsule provide a clear understanding of their unique behavior in this restricted medium. Because of the rigidity of the medium, these structures although generated in the ground state can rationalize the photochemical behavior of the molecules in the excited state.

Structural characterization of an intrinsically disordered protein complex using integrated small-angle neutron scattering and computing.

Characterizing structural ensembles of intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins is essential for studying structure-function relationships. Due to the different neutron scattering lengths of hydrogen and deuterium, selective labeling and contrast matching in small-angle neutron scattering (SANS) becomes an effective tool to study dynamic structures of disordered systems. However, experimental timescales typically capture measurements averaged over multiple conformations, leaving complex SANS data for disentanglement. We hereby demonstrate an integrated method to elucidate the structural ensemble of a complex formed by two IDRs. We use data from both full contrast and contrast matching with residue-specific deuterium labeling SANS experiments, microsecond all-atom molecular dynamics (MD) simulations with four molecular mechanics force fields, and an autoencoder-based deep learning (DL) algorithm. From our combined approach, we show that selective deuteration provides additional information that helps characterize structural ensembles. We find that among the four force fields, a99SB-disp and CHARMM36m show the strongest agreement with SANS and NMR experiments. In addition, our DL algorithm not only complements conventional structural analysis methods but also successfully differentiates NMR and MD structures which are indistinguishable on the free energy surface. Lastly, we present an ensemble that describes experimental SANS and NMR data better than MD ensembles generated by one single force field and reveal three clusters of distinct conformations. Our results demonstrate a new integrated approach for characterizing structural ensembles of IDPs.