Structural Molecular Dynamics Research Articles

Proton inversion tunneling in the rotational spectrum of acetone cyanohydrin

Rotational transitions of gauche-acetone cyanohydrin are measured in the microwave range between 5 and 23 GHz. Results from quantum chemical calculations indicate that the hydrogen atom of the hydroxyl group undergoes a tunneling motion connecting two equivalent structures. The observed signals are assigned to the two lowest tunneling substates 0+ and 0-, which belong to either a- or c-type transitions exhibiting Coriolis splittings of a few MHz. Additional hyperfine structure arises from the quadrupole coupling 14N nucleus. The energy separation ΔE between the 0+ and 0- states is predicted to be around 50 GHz. The molecular structure and internal dynamics are discussed in terms of their spectral signatures.

Surface-enhanced ultrafast two-dimensional vibrational spectroscopy with engineered plasmonic nano-antennas.

Development of noble metal nanostructure substrates that provide strong near-field enhancements enables applications of linear and nonlinear infrared (IR) spectroscopies to study minute sample quantities, such as nanometer thick films and molecular monolayers. Large near-field enhancements of the electric fields used for spectroscopic interrogation of molecules at the nanostructure surface result in enhancement of the spectroscopic signatures. This enhancement scales with the nonlinear order of the method, providing particularly large signal gains for third- and fifth-order IR methods, reaching 106 and 108 raw enhancement factors, not adjusted to the amount of interrogated sample. In this perspective, we overview the advances in the development of nano-arrays of antenna-like nanostructures for mid-IR measurements and illustrate their use in linear and especially nonlinear two-dimensional IR approaches. We discuss how studies of the interaction mechanisms between light, plasmonic antennas, and molecular excitations benefit from the nonlinear two-dimensional time-resolved methods, which involve high-order scaling of the signal with the excitation field, high sensitivity to signal localization, and coherence of the excitation over a broad bandwidth. On the other hand, we demonstrate how studies of molecular structure and ultrafast dynamics by these advanced spectroscopic methods benefit from surface enhancement of signals by plasmonic antennas.

Molecular Structural Dynamics Captured with Ultrafast Electron Diffraction

Molecular Structural Dynamics Captured with Ultrafast Electron Diffraction

Formation of Gaseous Proteins via the Ion Evaporation Model (IEM) in Electrospray Mass Spectrometry.

The mechanisms whereby protein ions are released into the gas phase from charged droplets during electrospray ionization (ESI) continue to be controversial. Several pathways have been proposed. For native ESI the charged residue model (CRM) is favored; it entails the liberation of proteins via solvent evaporation to dryness. Unfolded proteins likely follow the chain ejection model (CEM), which involves the gradual expulsion of stretched-out chains from the droplet. According to the ion evaporation model (IEM) ions undergo electrostatically driven desorption from the droplet surface. The IEM is well supported for small precharged species such as Na+. However, it is unclear whether proteins can show IEM behavior as well. We examined this question using molecular dynamics (MD) simulations, mass spectrometry (MS), and ion mobility spectrometry (IMS) in positive ion mode. Ubiquitin was chosen as the model protein because of its structural stability which allows the protein charge in solution to be controlled via pH adjustment without changing the protein conformation. MD simulations on small ESI droplets (3 nm radius) showed CRM behavior regardless of the protein charge in solution. Surprisingly, many MD runs on larger droplets (5.5 nm radius) culminated in IEM ejection of ubiquitin, as long as the protein carried a sufficiently large positive solution charge. MD simulations predicted that nonspecific salt adducts are less prevalent for IEM-generated protein ions than for CRM products. This prediction was confirmed experimentally. Also, collision cross sections of MD structures were in good agreement with IMS data. Overall, this work reveals that the CRM, CEM, and IEM all represent viable pathways for generating gaseous protein ions during ESI. The IEM is favored for proteins that are tightly folded and highly charged in solution and for droplets in a suitable size regime.

The crystal structure of tetrameric copper(II) complexes, Hirshfeld surface analysis, and vector analyses of Cu4OCl6L4 complexes with N-donor ligands

It is known, that in the Cu4OX6L4 (X = Cl, Br) complexes can be present many different ligands L, including bioligands. The synthesis and characterization of Cu4OBCl6(ron)4 (1) and Cu4OCl6(3-Mepy)4 (2) (where ron is ronicol or 3-methanolpyridine and 3-Mepy is 3-methylpyridine) are reported. The complexes under study were X-ray structure analysis and Hirshfeld surface analysis. Tetranuclear Cu4OX6L4 complexes with molecular structure (Fig. 1) can help to better understand the role of donor–acceptor and electron-transfer properties in copper proteins. The coordination sphere about each copper(II) atom is trigonal bipyramidal with three chlorine atoms in the equatorial plane. The apical positions are occupied by the central oxygen atom and the nitrogen atom of the respective ligand (CuCl3ON). Here are studied chloridocomplexes of some N-donor ligands, L = chloro-promazine, ronicol (3-pyridylmethanol), 2-ethylpyrazine, seven derivatives of pyrazol and for comparisons 3-methylpyridine. The Cu4OCl6L4 molecule is regarded as a supramolecular model of interactions between bioligand L and hypothetical “round-shaped” coordination tetra-receptor Cu4OCl6. Vector calculations applied usualy to mechanical and electrical macroconstructions are here applied to microconstructions represented by structures of Cu4OX6L4 molecules. For vector calculations each Cu4OX6L4 structure is placed (Fig. 1) into the three-dimensional Cartesian coordinate system with the central oxygen atom O1 placed in its origin 0. Studied bioligands are compared and described by molecular structural dynamics and corresponding shifts of electron densities by means of bond lenghts (O1–Cu, Cu–L, Cu–X) and structural distances (O1···X, O1···L).

Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening

Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from “up” to “down” conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below –8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak. Communicated by Ramaswamy H. Sarma

The Dual-Targeting Activity of the Metabolite Substrate of Para-amino Salicyclic Acid in the Mycobacterial Folate Pathway: Atomistic and Structural Perspectives

Therapeutic targeting of folate biosynthetic pathway has recently been explored as a viable strategy in the treatment of tuberculosis. The bioactive metabolite substrate of Para-amino salicyclic acid (PAS-M) reportedly dual-targets dihydrofolate reductase (DHFR) and flavin-dependent thymidylate synthase (FDTS), two essential enzymes in folate biosynthetic pathway. However, the molecular mechanisms and structural dynamics of this dual inhibitory activity of the PAS-M remain elusive. Molecular dynamics simulations revealed that binding of PAS-M towards DHFR is characterized by a recurrence of strong conventional hydrogen bond interactions between a peculiar DHFR binding site residue (Asp27) and the 2-amino-decahydropteridin-4-ol group of PAS-M. Similarly, the binding of PAS-M towards FDTS also involved consistent strong conventional hydrogen bond interactions between some specific residues (Tyr101, Arg172, Thr4, Gln103, Arg87 and Gln106) and, the 2-amino-decahydropteridin-4-ol group, thus establishing the cruciality of the group. Structural dynamics of the bound complexes of both enzymes revealed that, upon binding, PAS-M is anchored at the entrance of hydrophobic pockets by strong hydrogen bond interactions while the rest of the structure gains access to deeper hydrophobic residues to engage in favorable interactions. Further analysis of atomistic changes of both enzymes showed increased C-α atom deviations as well as an increase C-α atoms radius of gyration consistent with structural disorientations. These conformational changes possibly interfered with the biological functions of the enzymes and hence their inhibition as experimentally reported. Structural Insights provided could open up a novel paradigm of structure-based design of multi-targeting inhibitors of biological targets in the folate biosynthetic pathway toward tuberculosis therapy.

Lipid‐Embedded Molecular Dynamics Simulation Model for Exploring the Reverse Prostaglandin D2 Agonism of CT‐133 towards CRTH2 in the Treatment of Type‐2 Inflammation Dependent Diseases

Chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2) has been involved in several inflammation dependent diseases by mediating the chemotaxis of pro-inflammatory cells in response to allergy and other responses through PGD2 ligation. This CRTH2-PGD2 signaling pathway has become a target for treating allergic and type 2 inflammation dependent diseases, with many inhibitors developed to target the PGD2 binding pocket. One of such inhibitors is the ramatroban analog, CT-133, which exhibited therapeutic potency cigarette smoke-induced acute lung injury in patients. Nonetheless, the molecular mechanism and structural dynamics that accounts for its therapeutic prowess remain unclear. Employing computational tools, this study revealed that although the carboxylate moiety in CT-133 and the native agonist PGD2 aided in their stability within the CRTH2 binding pocket, the tetrahydrocarbazole group of CT-133 engaged in strong interactions with binding pocket residues which could have formed as the basis of the antagonistic advantage of CT-133. Tetrahydrocarbazole group interactions also enhanced the relative stability CT-133 within the binding pocket which consequently favored CT-133 binding affinity. CT-133 binding also induced an inactive or 'desensitized' state in the helix 8 of CRTH2 which could conversely favor the recruitment of arrestin. These revelations would aid in the speedy development of small molecule inhibitors of CRTH2 in the treatment of type 2 inflammation dependent diseases.

Molecular level nucleation mechanisms of hierarchical MFI and MOR zeolite structures via non-stochastic pathways.

Understanding the chemical mechanism of crystal nucleation at the molecular level is crucial for the design of architectural structures of valuable materials in the future. In this study, it has been revealed that amorphous silicate precursors, which play a role in the nucleation processes of zeolitic frameworks, can be regularly fragmented in mass spectroscopy due to the hydroxyl functional groups in their molecular structures. In this way, by using the mass spectra acquired from LDI-TOF MS, the systematic evolution stages of a common 1D precursor converting to the 3D unit cells of MFI and MOR zeolite structures observed in the same reaction medium were constructed through a nucleation mechanism at the molecular level for the first time. Here we show a novel nucleation pathway that does not occur via stochastic assembly of atoms or distinct building blocks by molecular recognition. Each of the proposed nucleation mechanisms of these different frameworks carrying structural similarities is from different combinations of sequential self-attaching intramolecular covalent couplings of identical origin precursors. The dynamic molecular structure capable of forming finite building units of target frameworks during the nucleation process of this precursor, which is the polymerized form of simple 6-membered siloxane chains, has been arranged around structure directing agents before a hydrothermal reaction.

Excited state proton transfer processes of pyranine studied by femtosecond stimulated Raman spectroscopy

As one of the most fundamental processes, proton transfer reaction plays an important role in chemical and biological process, and to reveal the choreography of the proton motion intra- and intermolecularly, a spectroscopic technique capable of capturing molecular structural dynamics of excited-state proton transfer motions on an intrinsic time scale is needed. In this study, We utilize wavelength-tunable femtosecond stimulated Raman spectroscopy with a time resolution of ~100 fs, spectral resolution of 15 cm<sup>–1</sup> and spectral range of 400 cm<sup>–1</sup>—1800 cm<sup>–1</sup>, combined with traditional transient absorption spectroscopywith a time window between 0 and 600 ps to simultaneously achieve reaction dynamics for transient reactant and product of the photoacid pyranine (8-hydroxypyrene1, 3, 6-trisulfonic acid, HPTS) molecules undergoing excited-state proton transfer reaction in complex with water and acetate molecules. Marker bands attributed to the deprotonated form of HPTS in a frequency range from 400 cm<sup>–1</sup> to 1700 cm<sup>–1</sup> are obtained under the excitation of 400 nm laser pulses. The marker band at 1516 cm<sup>–1</sup>, which is assigned to phenolic ring carbon carbon double band stretching accompanied with carbon hydrogen in-plane rocking motions, exhibits complex rise and decay dynamics. The simultaneously observed excited-state Raman mode at 920 cm<sup>–1</sup> which is assigned to the excited carbon-carbon single bond stretch mode in the protonated acetic acid root molecule, helps us to clearly resolve the reaction rates of excited-state proton transfer. Based on the multi-exponential fitting results, the dynamics of excited-state Raman mode at 920 cm<sup>–1</sup> exhibits bi-exponential processes with time constants of ~470 fs and ~3 ps. The ultrafast time component indicates that the excited-state proton transfer originates from an HPTS-acetate complex, indicating that part of the ground-state HPTS molecules are in the “tight” hydrogen bonding configuration that can quickly shift the excited-state proton charge toward the acetate acceptor molecule through a direct hydrogen bond. The second slower time component implies a significant subpopulation of HPTS in the ground state, i.e. hydrogen bonds to an acetate ion via an intervening water molecule, and upon photo excitation, the proton transfers to the water solvent before proton is picked up by the acetate ion.

Improved molecular structure retrieval method for photoelectron holography

Photoelectron holography is a method that retrieves molecular structure information from photoelectron diffraction patterns generated by x-ray free-electron lasers, which have the promise of following dynamic molecular structure evolutions with angstrom spatial and femtosecond temporal resolutions (the so-called molecular movie). However, an additional phase is introduced when the photoelectron is scattered by an atom, and this scattering phase turns into a spatial error when the position of the atom is retrieved using a Fourier-type transform. We propose a method to remove, or greatly suppress, this error, with demonstrations using numerical examples.

The new ball-type zinc phthalocyanine with S[sbnd]S bridge; Synthesis, computational and photophysicochemical properties

In this study, the starting compound 4,4′-disulfanediyldiphthalonitrile (1) and its ball-type zinc phthalocyanine (2) were synthesized and characterized by standard spectroscopic methods. The molecular structure and supramolecular dynamics of the compound (1) have been investigated by the analysis of the single crystal X-ray diffraction data. To further understand the intermolecular interactions of compound (1), the Hirshfeld surface analysis has been carried out. The compound (1) and (2) were investigated by quantum chemical calculations. Their quantum chemical parameters such as highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), chemical hardness were performed by B3lyp, HF, M062x method. The ΔG values of the compound (1) and (2) were calculated by using the obtained results. The calculated Infrared spectroscopy, Nuclear Magnetic Resonance, and UV–vis spectra of the compounds were investigated. In addition, photophysical (fluorescence quantum yields) and photochemical (singlet oxygen generation and photodegradation under light irradiation) properties of newly synthesized ball-type zinc phthalocyanine (2) were investigated in dimethyl sulfoxide (DMSO) solutions. We obtained very high singlet oxygen quantum yields as 0.89, suggesting its potential as photosensitizer in PDT treatment.

Influence of Expertise on Perception and Understanding on Viewing a Molecular Animation of the Lung Endothelial Surface Layer and its Role in Inflammation

At the University of Illinois College of Medicine Anesthesiology Research department, lung trauma researchers aimed to generate interest in the importance of the lung endothelial surface layer in inflammation. However, they had difficulty describing the dynamic molecular structure of the lung endothelial surface layer and its role in inflammatory processes in the lung. A 3D animation was created because of its ability to communicate a rich and complex molecular narrative. Prior studies have shown that, for scientific animations, level of expertise of the viewer influences how an animation is perceived. This study aimed to improve lung trauma researchers’ ability to generate interest in their research and to assess if prior knowledge affects how biomedical animations are perceived in terms of engagement by analyzing eye-tracking.

Unsupervised and Supervised Learning over theEnergy Landscape for Protein Decoy Selection.

The energy landscape that organizes microstates of a molecular system and governs the underlying molecular dynamics exposes the relationship between molecular form/structure, changes to form, and biological activity or function in the cell. However, several challenges stand in the way of leveraging energy landscapes for relating structure and structural dynamics to function. Energy landscapes are high-dimensional, multi-modal, and often overly-rugged. Deep wells or basins in them do not always correspond to stable structural states but are instead the result of inherent inaccuracies in semi-empirical molecular energy functions. Due to these challenges, energetics is typically ignored in computational approaches addressing long-standing central questions in computational biology, such as protein decoy selection. In the latter, the goal is to determine over a possibly large number of computationally-generated three-dimensional structures of a protein those structures that are biologically-active/native. In recent work, we have recast our attention on the protein energy landscape and its role in helping us to advance decoy selection. Here, we summarize some of our successes so far in this direction via unsupervised learning. More importantly, we further advance the argument that the energy landscape holds valuable information to aid and advance the state of protein decoy selection via novel machine learning methodologies that leverage supervised learning. Our focus in this article is on decoy selection for the purpose of a rigorous, quantitative evaluation of how leveraging protein energy landscapes advances an important problem in protein modeling. However, the ideas and concepts presented here are generally useful to make discoveries in studies aiming to relate molecular structure and structural dynamics to function.

Multiply charged energetic metal ion emissions from dinuclear metal complex exposed to intense femtosecond laser fields

Coulomb explosion of nonmetal ions emerged from a variety of molecules has been studied and utilized for the determination of molecular structure and reaction dynamics. In contrast, Coulomb explosion of metal ions, particularly the large Coulombic interactions are expected, has not yet been explored. In this study, the angular distributions of Mnx+ (x = 1–5), Cy+ (y = 1–4), and Oz+ (z = 1–3) emerged from dimanganese decacarbonyl, in which two metal atoms are sandwiched by axial ligands, exposed to intense femtosecond laser fields (1 × 1014–3 × 1015 W cm−2) are investigated. Manganese ions are produced at relatively low laser intensity compared with other transition metal ions with the same charge number but emerged from mononuclear complexes such as metallocenes and metal hexacarbonyls. The kinetic energies of Mn4+ and Mn5+ are described by the simple Coulomb repulsion model of manganese dimer ion. Fairly high kinetic energy of oxygen and carbon ions compared with those emerged from metal hexacarbonyls strongly suggests that atomic ions originating in ligands are repelled by manganese ions at the moment of Coulomb explosion. The use of dinuclear metal complex is advantageous in the production of multiply charged metal ions accompanying high kinetic energy since two manganese ions are in close confinement due to the repulsions with axial ligand (atomic) ions.

Insight into the role of pre-assembly and desolvation in crystal nucleation: a case of p-nitrobenzoic acid.

As one of the most important phenomena in crystallization, the crystal nucleation process has always been the focus of research. In this work, influences of pre-assembly species and the desolvation process on the crystal nucleation process were studied. p-Nitrobenzoic acid (PNBA) was taken as a model compound to investigate the relationship between solution chemistry and nucleation kinetics in seven different solvents. One unsolvated form and four solvates of PNBA were obtained and one of the solvates was newly discovered. The nucleation behaviours and nucleation kinetics of PNBA in the seven solvents were studied and analyzed. Density functional theory (DFT) and solvation energy calculation were adopted to evaluate the strength of solute-solvent interactions. Vibrational spectroscopy combined with molecular simulation was applied to reveal the pre-assembly species in the solution. Based on these results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics was proposed and discussed. It was found that the structural similarity between solution chemistry and crystal structure, the interaction between specific sites and the overall strength of solvation will jointly affect the nucleation process.

Molecular cloning, gene expression analysis, and in silico characterization of UDP-N-acetylglucosamine pyrophosphorylase from Bombyx mori.

The present study was aimed to explore the molecular and structural features of UDP-N-acetylglucosamine pyrophosphorylase of Bombyx mori (BmUAP), an essential enzyme for chitin synthesis in insects. The BmUAP cDNA sequence was cloned and expression profiles were monitored during the molting and feeding stages of silkworm larvae. The effect of 20-hydroxyecdysone (20E) on BmUAP expression, and on silkworm molting was studied, which revealed that 20E regulates its expression. Multiple sequence alignment of various pyrophosphorylases revealed that the residues N223, G290, N327, and K407 of human UAP (PDB ID: 1JV1) were found to be highly conserved in BmUAP and all other eukaryotic UAPs considered for the study. Phylogenetic analysis inferred that the UAPs possess discrete variations in primary structure among different insect Orders while sharing good identity between species of the Order. The structure of BmUAP was predicted and its interactions with uridine triphosphate, N-acetylglucosamine-1-phosphate, and UDP-N-acetylglucosamine were analyzed. Virtual screening with a library of natural compounds resulted in five potential hits with good binding affinities. On further analysis, these five hits were found to be mimicking substrate and product, in inducing conformational changes in the active site. This work provides crucial information on molecular interactions and structural dynamics of insect UAPs.

Molecular dynamics simulation investigation of the microwave heating supercritical water

Nonequilibrium NVE molecular dynamics (MD) simulations were performed to investigate the heating process of supercritical water (SCW) by the microwaves (the field intensities are from 3 × 105V/m to 3 × 109V/m with the frequencies of 915 MHz and 2.45 GHz, respectively). The energy distribution, microscopic molecular structure, diffusivity and hydrogen bond dynamics were analyzed. Microwaves field dependence on the rotational and translational coupling mechanisms of water molecules have been detected. The microwave energy has been converted to the kinetic and intermolecular energies of water. There are about 40% absorbed microwave energy is stored as the intermolecular energy, and the proportion decline at higher field intensity. The diffusion of supercritical water is non-linearly fluctuation due to the coupling of rotation and translation motions. And this work may provide a theoretical basis to improve the efficiency of industrial application with microwave and SCW.

Promoter Recognition: Putting TFIID on the Spot.

Basal transcription factor TFIID connects transcription activation to the assembly of the RNA polymerase II preinitiation complex at the core promoter of genes. The mechanistic understanding of TFIID function and dynamics has been limited by the lack of high-resolution structures of the holo-TFIID complex. Recent cryo-electron microscopy studies of yeast and human TFIID complexes provide insight into the molecular organization and structural dynamics of this highly conserved transcription factor. Here, we discuss how these TFIID structures provide new paradigms for: (i) the dynamic recruitment of TFIID; (ii) the binding of TATA-binding protein (TBP) to promoter DNA; (iii) the multivalency of TFIID interactions with (co)activators, nucleosomes, or promoter DNA; and (iv) the opportunities for regulation of TBP turnover and promoter dynamics.

PEG hydration and conformation in aqueous solution: Hints to macromolecular crowding

The molecular structural dynamics of PEG in aqueous solution has been addressed with a series of experimental data correlating macroscopic solution properties of PEG with structural and hydration properties at molecular level, by using thermodynamic, UV Brillouin and Raman spectroscopy data. Water activity measured in PEG 600 solutions by a novel dynamical calorimetry approach shows that data reveal some non-equilibrium process for dilute solutions. Brillouin scattering data on aqueous solutions in the UV range made possible the measurement of the viscoelastic relaxation of the system with a characteristic temperature, TM, as precursor of the glass transition process at lower T, while at constant temperature, the addition of water to liquid PEG 600 first lead to a slight decrease and then to an increase in the solution viscoelastic relaxation consistent with the slowest polymer dynamics observed in the concentrated solution. Specific Raman bands corresponding to trans and gauche conformations of the C–C and C–O bonds and their sequences in the PEG chain have been identified and their relative intensities as a function of concentration evidence non-monotonous variations with a rather unusual concentration dependence for the frequency of C–O bonds in the range of physiological temperatures.The heuristic result is that the extended time-space domains approach suggests an overall quasi-regular solution behavior of semidilute PEG, with opposite concentration dependence at low and at high water content, similar to discontinuities observed in excess thermodynamic properties and eutectic phase diagram. The cross-over of these distinct behaviors occurs at the concentration close to that usually employed to mimic the cellular crowding in biomolecular systems, highlighting the interplay of water molecules in solute-solute interactions.