Quantum Mechanics/molecular Mechanics Research Articles

Activation of Cryptochrome 4 from Atlantic Herring

Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.

Structure and Ultrafast X-ray Diffraction of the Hydrated Metaphosphate.

We study the pathway of metaphosphate hydration when a metaphosphate anion is dissolved in liquid water with an explicit water model. For this purpose, we propose a sequential Monte Carlo algorithm incorporated with the ab initio quantum mechanics/molecular mechanics (QM/MM) method, which can reduce the amount of ab initio QM/MM sampling while retaining the accuracy of the simulation. We demonstrate the numerical calculation of the standard enthalpy change for the successive addition reaction PO3-·2H2O + H2O ⇌ PO3-·3H2O in the liquid phase, which helps to clarify the hydration pathway of the metaphosphate. With the obtained hydrated structure of the metaphosphate anion, we perform ab initio calculations for its relaxation dynamics upon vibrational excitation and characterize the energy transfer process in solution with simulated ultrafast X-ray diffraction signals, which can be experimentally implemented with X-ray free-electron lasers.

Role of Bridging Groups in Regulating the Luminescence and Charge Transfer Properties of Thermally Activated Delayed Fluorescence Molecules: A Theoretical Perspective.

Organic emitters with a simultaneous combination of aggregation-induced emission (AIE) and thermally activated delayed fluorescence (TADF) characteristics are in great demand due to their excellent comprehensive performances toward efficient organic light-emitting diodes (OLEDs), biomedical imaging, and the telecommunications field. However, the development of efficient AIE-TADF materials remains a substantial challenge. In this work, light-emitting properties of two AIE-TADF molecules with different bridging groups ICz-BP and ICz-DPS are theoretically investigated in the solid state with the combined quantum mechanics/molecular mechanics (QM/MM) method and the thermal vibration correlation function (TVCF) theory. The research indicates that the C═O bridging bond in ICz-BP is more favorable than the S═O bridging bond in ICz-DPS for enhancing the planarity of the acceptor, increasing conjugation, and thereby elevating the transition dipole moment density. Simultaneously, the stacking pattern of ICz-BP in the solid facilitates a reduction in energy gap between S1 and T1 (ΔEST), achieving rapid reverse intersystem crossing rate (kRISC). Furthermore, compared to toluene, the stacking patterns of ICz-BP and ICz-DPS in the solid effectively suppress the out-of-plane wagging vibration of the acceptor, thereby inhibiting the loss of nonradiative energy in the excited state and realizing aggregation-induced emission. Moreover, the charge transport properties of both electrons and holes in ICz-BP are found to be higher than the corresponding rates in ICz-DPS, attributed to the smaller internal reorganization energy of ICz-BP in the solid state. Additionally, the calculations reveal a more balanced charge transport characteristic in ICz-BP, contributing to efficient exciton recombination and emission and ultimately mitigating efficiency roll-off. Based on these computational results, we aim to unveil the relationship between molecular structure and light-emitting properties, aiding in the design and development of efficient AIE-TADF devices.

Multiscale calculations reveal new insights into the reaction mechanism between KRASG12C and α, β-unsaturated carbonyl of covalent inhibitors

Utilizing α,β-unsaturated carbonyl group as Michael acceptors to react with thiols represents a successful strategy for developing KRASG12C inhibitors. Despite this, the precise reaction mechanism between KRASG12C and covalent inhibitors remains a subject of debate, primarily due to the absence of an appropriate residue capable of deprotonating the cysteine thiol as a base. To uncover this reaction mechanism, we first discussed the chemical reaction mechanism in solvent conditions via density functional theory (DFT) calculation. Based on this, we then proposed and validated the enzymatic reaction mechanism by employing quantum mechanics/molecular mechanics (QM/MM) calculation. Our QM/MM analysis suggests that, in biological conditions, proton transfer and nucleophilic addition may proceed through a concerted process to form an enolate intermediate, bypassing the need for a base catalyst. This proposed mechanism differs from previous findings. Following the formation of the enolate intermediate, solvent-assisted tautomerization results in the final product. Our calculations indicate that solvent-assisted tautomerization is the rate-limiting step in the catalytic cycle under biological conditions. On the basis of this reaction mechanism, the calculated kinact/ki for two inhibitors is consistent well with the experimental results. Our findings provide new insights into the reaction mechanism between the cysteine of KRASG12C and the covalent inhibitors and may provide valuable information for designing effective covalent inhibitors targeting KRASG12C and other similar targets.

HYSCORE and QM/MM Studies of Second Sphere Variants of the Type 1 Copper Site in Azurin: Influence of Mutations on the Hyperfine Couplings of Remote Nitrogens.

Secondary coordination sphere (SCS) interactions have been shown to play important roles in tuning reduction potentials and electron transfer (ET) properties of the Type 1 copper proteins, but the precise roles of these interactions are not fully understood. In this work, we examined the influence of F114P, F114N, and N47S mutations in the SCS on the electronic structure of the T1 copper center in azurin (Az) by studying the hyperfine couplings of (i) histidine remote Nε nitrogens and (ii) the amide Np using the two-dimensional (2D) pulsed electron paramagnetic resonance (EPR) technique HYSCORE (hyperfine sublevel correlation) combined with quantum mechanics/molecular mechanics (QM/MM) and DLPNO-CCSD calculations. Our data show that some components of hyperfine tensor and isotropic coupling in N47SAz and F114PAz (but not F114NAz) deviate by up to ∼±20% from WTAz, indicating that these mutations significantly influence the spin density distribution between the CuII site and coordinating ligands. Furthermore, our calculations support the assignment of Np to the backbone amide of residue 47 (both in Asn and Ser variants). Since the spin density distributions play an important role in tuning the covalency of the Cu-Scys bond of Type 1 copper center that has been shown to be crucial in controlling the reduction potentials, this study provides additional insights into the electron spin factor in tuning the reduction potentials and ET properties.

Breaking Down Resistance: Verapamil-Derived Compounds Augment Antibiotic Activity against Streptococcus Pneumonia via MATE Transporter Interference.

Pneumonia, an infectious lung disease, is a significant global health concern, claiming the lives of 740,180 children in 2019, which accounts for 14% of pediatric deaths. Recently, the management of pediatric pneumonia has become complex due to exposure to indoor and outdoor environmental toxins. Notably, exposure to pollutants and antibiotic-resistant bacteria during community and hospital-acquired pneumonia poses a serious threat to patient outcomes. The development of antibiotic resistance against Streptococcus pneumoniae is driven by the DinF efflux pump protein, which expels antibiotics from bacterial cells, leading to multidrug resistance. Therefore, blocking DinF could serve as a strategy to combat antibiotic resistance. This study aimed to identify DinF inhibitors from compounds analogous to verapamil, a well-known DinF inhibitor, through computational techniques including molecular docking, molecular dynamics simulations, ADMET analysis, MMGBSA, quantum mechanics, and Network Pharmacology. After considering docking scores, results of MMGBSA, quantum mechanics, Molecular Dynamics Simulations, ADMET analysis and network pharmacology profiling four compounds namely netarsudil, rimegepant, GSK-1521498 and tariquidar were found as the most promising DinF inhibitors. Therefore, these compounds hold a great promise as leads to the development of potent DinF inhibitors; however, further studies are needed to warrant their clinical uses against antibiotic resistant Streptococcus pneumonia-induced pneumonia.

Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib.

Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.

Analyzing fine scaling quantum effects on the buckling of axially-loaded carbon nanotubes based on the density functional theory and molecular mechanics method

In this paper, the quantum effects of fine scaling on the buckling behavior of carbon nanotubes (CNTs) under axial loading are investigated. Molecular mechanics and quantum mechanics are respectively utilized to study the buckling behavior and to obtain the molecular mechanics coefficients of fine-scale nanotubes. The results of buckling behavior of CNTs with different chiralities with finite and infinite dimensions are given, and a comparison study is presented on them. The differences between finite and infinite nanotubes reflect the quantum effects of fine scaling on the buckling behavior. In addition, the results show that the dimensional changes highly affect the mechanical properties and the buckling behavior of CNTs to certain dimensions. Moreover, dimensional changes have a significant effect on the critical buckling strain. Beside, in addition to the structure dimensions, the arrangement of structural and boundary atoms have a major influence on the buckling behavior.

Redox Properties of Flavin in BLUF and LOV Photoreceptor Proteins from Hybrid QM/MM Molecular Dynamics Simulation.

Flavins play an important role in many oxidation and reduction processes in biological systems. For example, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) are common cofactors found in enzymatic proteins that use the special redox properties of these flavin molecules for their catalytic or photoactive functions. The redox potential of the flavin is strongly affected by its (protein) environment; however, the underlying molecular interactions of this effect are still unknown. Using hybrid quantum mechanics/molecular mechanics (QM/MM) simulation techniques, we have studied the redox properties of flavin in the gas phase, aqueous solution, and two different protein environments, in particular, a BLUF and a LOV photoreceptor domain. By mapping the changes in electrostatic potential and solvent structure, we gain insight into how specific polarization of the flavin by its environment tunes the reduction potential. We find also that accurate calculation of the reduction potentials of these systems by using the hybrid QM/MM approach is hampered by a too limited sampling of the counterion configurations and by artifacts at the QM/MM boundary. We make suggestions for how these issues can be overcome.

Modeling solvent effects and convergence of 31P-NMR shielding calculations with COBRAMM.

Solvent effects on 31P-NMR parameters for triphenylphosphine oxide and triphenylphosphine in chloroform have been extensively investigated by testing different solvation models. The solvent is described implicitly, mixed implicitly/explicitly, and using full explicit models. Polarizable continuum model (PCM), molecular dynamic (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations are used to disclose the effects of solute/solvent interactions and, more generally, the role of the embedding in NMR simulations. The results show the beneficial effect of carrying out QM/MM optimizations on top of geometries directly extracted from classical MD simulations, used to ensure representative conformational sampling. The nuclear shielding convergence has been tested against a different number of snapshots and with the inclusion of solvent shells into the QM region. An automated MD//QM/MM//GIAO protocol, implemented in the COBRAMM package, is here proposed and tested on trimethyl phosphite showing that our approach boosts the convergence of nuclear shielding satisfactorily. The present work aims to be a stepping-stone to assess proper QM/MM computational strategies in simulating chemical shifts in non-homogeneous systems like supramolecular and biological systems.

Systematic QM/MM Study for Predicting 31P NMR Chemical Shifts of Adenosine Nucleotides in Solution and Stages of ATP Hydrolysis in a Protein Environment.

NMR (nuclear magnetic resonance) spectroscopy allows for important atomistic insights into the structure and dynamics of biological macromolecules; however, reliable assignments of experimental spectra are often difficult. Herein, quantum mechanical/molecular mechanical (QM/MM) calculations can provide crucial support. A major problem for the simulations is that experimental NMR signals are time-averaged over much longer time scales, and since computed chemical shifts are highly sensitive to local changes in the electronic and structural environment, sufficiently large averages over representative structural ensembles are essential. This entails high computational demands for reliable simulations. For NMR measurements in biological systems, a nucleus of major interest is 31P since it is both highly present (e.g., in nucleic acids) and easily observable. The focus of our present study is to develop a robust and computationally cost-efficient framework for simulating 31P NMR chemical shifts of nucleotides. We apply this scheme to study the different stages of the ATP hydrolysis reaction catalyzed by p97. Our methodology is based on MM molecular dynamics (MM-MD) sampling, followed by QM/MM structure optimizations and NMR calculations. Overall, our study is one of the most comprehensive QM-based 31P studies in a protein environment and the first to provide computed NMR chemical shifts for multiple nucleotide states in a protein environment. This study sheds light on a process that is challenging to probe experimentally and aims to bridge the gap between measured and calculated NMR spectroscopic properties.

The catalytic mechanism of the RNA methyltransferase METTL3.

The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on messenger RNA (mRNA) in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a BA representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release, and suggests that the latter step is rate-limiting for METTL3. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.

The catalytic mechanism of the RNA methyltransferase METTL3

The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on messenger RNA (mRNA) in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a BA representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release, and suggests that the latter step is rate-limiting for METTL3. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.

Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins.

High binding affinity and selectivity of metal ions are essential to the function of metalloproteins. Thus, understanding the factors that determine these binding characteristics is of major interest for both fundamental mechanistic investigations and guiding of the design of novel metalloproteins. In this work, we perform QM cluster model calculations and quantum mechanics/molecular mechanics (QM/MM) free energy simulations to understand the binding selectivity of Ca2+ and Mg2+ in the wild-type carp parvalbumin and its mutant. While a nonpolarizable MM model (CHARMM36) does not lead to the correct experimental trend, treatment of the metal binding site with the DFTB3 model in a QM/MM framework leads to relative binding free energies (ΔΔGbind) comparable with experimental data. For the wild-type (WT) protein, the calculated ΔΔGbind is ∼6.6 kcal/mol in comparison with the experimental value of 5.6 kcal/mol. The good agreement highlights the value of a QM description of the metal binding site and supports the role of electronic polarization and charge transfer to metal binding selectivity. For the D51A/E101D/F102W mutant, different binding site models lead to considerable variations in computed binding affinities. With a coordination number of seven for Ca2+, which is shown by QM/MM metadynamics simulations to be the dominant coordination number for the mutant, the calculated relative binding affinity is ∼4.8 kcal/mol, in fair agreement with the experimental value of 1.6 kcal/mol. The WT protein is observed to feature a flexible binding site that accommodates a range of coordination numbers for Ca2+, which is essential to the high binding selectivity for Ca2+ over Mg2+. In the mutant, the E101D mutation reduces the flexibility of the binding site and limits the dominant coordination number of Ca2+ to be seven, thereby leading to reduced binding selectivity against Mg2+. Our results highlight that the binding selectivity of metal ions depends on both the structural and dynamical properties of the protein binding site.

Amazon Plant‐Derived Compounds Suppressing Dengue NS5 Protein: Insights from Computational Drug Development and Network Pharmacology Approach

AbstractDengue, a life‐threatening Flavivirus infection, is rampant across 128 tropical and subtropical regions, annually afflicting millions and causing 20,000 deaths due to inadequate treatments. Despite the FDA‐approved Dengvaxia vaccine, its limitations necessitate novel drug development. Notably, the enzymatic nature of the NS5 protein (PDB ID: 3p97) within DENV, responsible for viral RNA synthesis, makes it a prime drug target. Employing Pharmacoinformatics, Molecular Dynamics Simulations, Quantum Mechanics, and network pharmacology, we screened compounds from NuBBE, the Brazilian Amazon Plant Database, along with reported dengue compounds. Docking yielded promising scores (−11.1 to −2.8) and (−11 to −3.1) kcal/mol, respectively. From 1310 phytochemicals, top compounds emerged: Ramosin, Pectolinarin, hinokinin, and sesamin, boasting scores of −11, −11, −9.7, and −9.6, surpassing Acetaminophen's −5.8. Validated post‐docking interactions used 100 ns Molecular Dynamics Simulations and quantum mechanics. Pharmacokinetics and Toxicity analysis aligned with ADME norms, showing no undue toxicity. Network pharmacology unveiled connections between bioactive chemicals and disease targets. This investigation uncovers the potential of these compounds to inhibit DENV‐3 NS5 protein. In vitro, in vivo, and cell line assays are crucial next steps for specific anti‐dengue drug development.

Fluoride Ion Binding and Translocation in the CLCF Fluoride/Proton Antiporter: Molecular Insights from Combined Quantum-Mechanical/Molecular-Mechanical Modeling.

CLCF fluoride/proton antiporters move fluoride ions out of bacterial cells, leading to fluoride resistance in these bacteria. However, many details about their operating mechanisms remain unclear. Here, we report a combined quantum-mechanical/molecular-mechanical (QM/MM) study of a CLCF homologue from Enterococci casseliflavus (Eca), in accord with the previously proposed windmill mechanism. Our multiscale modeling sheds light on two critical steps in the transport cycle: (i) the external gating residue E118 pushing a fluoride in the external binding site into the extracellular vestibule and (ii) an incoming fluoride reconquering the external binding site by forcing out E118. Both steps feature competitions for the external binding site between the negatively charged carboxylate of E118 and the fluoride. Remarkably, the displaced E118 by fluoride accepts a proton from the nearby R117, initiating the next transport cycle. We also demonstrate the importance of accurate quantum descriptions of fluoride solvation. Our results provide clues to the mysterious E318 residue near the central binding site, suggesting that the transport activities are unlikely to be disrupted by the glutamate interacting with a well-solvated fluoride at the central binding site. This differs significantly from the structurally similar CLC chloride/proton antiporters, where a fluoride trapped deep in the hydrophobic pore causes the transporter to be locked down. A free-energy barrier of 10-15 kcal/mol was estimated via umbrella sampling for a fluoride ion traveling through the pore to repopulate the external binding site.

Study of Interactions of Nucleoside Anticancer Drugs, Capecitabine and Gemcitabine, with SWNT and BNNT using Molecular and Quantum Mechanical Calculations

Abstract: Using single-wall carbon nanotubes (SWCNTs) and boron nitride nanotubes (BNNTs), this study evaluated the interactions between Capecitabine (CAP) and Gemcitabine (GEM). Molecular mechanics and quantum mechanics were used in the analysis. : The interaction between CP and GM with SWCNTs and BNNTs under various solvents was analyzed using the self-consistent reaction field (SCRF) as a model and DFT as the analytical method. Additionally, the effect of temperature on the stability of the molecule interactions during the experiment was examined. The thermodynamic properties of the title compounds were analyzed based on theoretical calculations. It included the calculation of Frontier Molecular Orbitals (FMOs) and Total Density of States (DOS). In addition to studying the ionization potential (I), we also examined the other molecular properties of the structures, such as electrophilicity (ω), electron affinity (A), chemical hardness (η), and electronic chemical potential (μ). To investigate the interaction between CAP and GEM with SWCNTs and BNNTs, molecular mechanics methods (MM) including AMBER, OPLS, CHARMM, and MM+ force fields, were employed. Monte Carlo simulation techniques were used to calculate the results at different temperatures. : The effects of the liquid phase and mixed solvent media with varying dielectric constants (Water, DMSO, Methanol, and Ethanol) on the interaction between CAP and GEM using the force fields described above were examined in this study. The correlation between data generated by Monte Carlo, Quantum Mechanics, and Molecular Mechanics was demonstrated. There was a striking similarity in the thermodynamic properties and conformer populations of all three materials.

QM/MM Study of the Catalytic Mechanism and Substrate Specificity of the Aromatic Substrate C-Methyltransferase Fur6.

In the field of medical chemistry and other organic chemistry, introducing a methyl group into a designed position has been difficult to achieve. However, owing to the vigorous developments in the field of enzymology, methyltransferases are considered potential tools for addressing this problem. Within the methyltransferase family, Fur6 catalyzes the methylation of C3 of 1,2,4,5,7-pentahydroxynaphthalene (PHN) using S-adenosyl-l-methionine (SAM) as the methyl donor. Here, we report the catalytic mechanism and substrate specificity of Fur6 based on computational studies. Our molecular dynamics (MD) simulation studies reveal the reactive form of PHN and its interactions with the enzyme. Our hybrid quantum mechanics/molecular mechanics (QM/MM) calculations suggest the reaction pathway of the methyl transfer step in which the energy barrier is 8.6 kcal mol-1. Our free-energy calculations with a polarizable continuum model (PCM) indicate that the final deprotonation step of the methylated intermediate occurs after it is ejected into the water solvent from the active center pocket of Fur6. Additionally, our studies on the protonation states, the highest occupied molecular orbital (HOMOs), and the energy barriers of the methylation reaction for the analogs of PHN demonstrate the mechanism of the specificity to PHN. Our study provides valuable insights into Fur6 chemistry, contributing to a deeper understanding of molecular mechanisms and offering an opportunity to engineer the enzyme to achieve high yields of the desired product(s).

Deciphering the structure of deep eutectic solvents: A computational study from the solute's viewpoint

In the last few years, Deep Eutectic Solvents (DESs) have emerged as sustainable alternatives to traditional organic solvents. The high degree of freedom when tailoring DES structures represents, at the same time, their most praised and most complicated feature. Indeed, given the enormous number of possible combinations, the selection of the most suitable DES for a given application cannot be based on a trial-and-error approach; therefore, reliable computational tools are needed to fully exploit DESs potentialities. In this work, we propose the first computational protocol to investigate absorption properties of solutes dissolved in DES. The protocol combines an accurate sampling of the solute-solvent phase-space by means of Molecular Dynamics (MD) and a fully atomistic Quantum Mechanics/Molecular Mechanics (QM/MM) approach to describe intermolecular interactions and spectral properties. In this way, specific interactions such as hydrogen bonding, which characterize DES complex interaction patterns, are properly modelled. The robustness and reliability of the method are proved by comparing computed data with experimental spectra of 2-hydroxymethylfurfural and syringic, vanillic, p-coumaric, gallic, and caffeic acids dissolved in DES and water. These molecules have been chosen because of their relevance in the frame of biomass valorization. Remarkably, the protocol allows getting insights into DES/water mixtures and opens up to the prediction of aqueous DES behaviour of the water threshold which causes the switch from water-in-DES to aqueous electrolyte-like environments.

Surface-Accelerated String Method for Locating Minimum Free Energy Paths.

We present a surface-accelerated string method (SASM) to efficiently optimize low-dimensional reaction pathways from the sampling performed with expensive quantum mechanical/molecular mechanical (QM/MM) Hamiltonians. The SASM accelerates the convergence of the path using the aggregate sampling obtained from the current and previous string iterations, whereas approaches like the string method in collective variables (SMCV) or the modified string method in collective variables (MSMCV) update the path only from the sampling obtained from the current iteration. Furthermore, the SASM decouples the number of images used to perform sampling from the number of synthetic images used to represent the path. The path is optimized on the current best estimate of the free energy surface obtained from all available sampling, and the proposed set of new simulations is not restricted to being located along the optimized path. Instead, the umbrella potential placement is chosen to extend the range of the free energy surface and improve the quality of the free energy estimates near the path. In this manner, the SASM is shown to improve the exploration for a minimum free energy pathway in regions where the free energy surface is relatively flat. Furthermore, it improves the quality of the free energy profile when the string is discretized with too few images. We compare the SASM, SMCV, and MSMCV using 3 QM/MM applications: a ribozyme methyltransferase reaction using 2 reaction coordinates, the 2'-O-transphosphorylation reaction of Hammerhead ribozyme using 3 reaction coordinates, and a tautomeric reaction in B-DNA using 5 reaction coordinates. We show that SASM converges the paths using roughly 3 times less sampling than the SMCV and MSMCV methods. All three algorithms have been implemented in the FE-ToolKit package made freely available.