Enhancing CO2 Hydrogenation Using a Heterogeneous Bimetal NiAl-Deposited Metal-Organic Framework NU-1000: Insights from First-Principles Calculations.

The hydrogenation of CO2 to high-value-added liquid fuels is crucial for greenhouse gas emission reduction and optimal utilization of carbon resources. Developing supported heterogeneous catalysts is a key strategy in this context, as they offer well-defined active sites for in-depth mechanistic studies and improved catalyst design. Here, we conducted extensive first-principles calculations to systematically explore the reaction mechanisms for CO2 hydrogenation on a heterogeneous bimetal NiAl-deposited metal-organic framework (MOF) NU-1000 and its catalytic performance as atomically dispersed catalysts for CO2 hydrogenation to formic acid (HCOOH), formaldehyde (H2CO), and methanol (CH3OH). The present results reveal that the presence of the NiAl-oxo cluster deposited on NU-1000 efficiently activates H2, and the facile heterolysis of H2 on Ni and adjacent O sites serves as a precursor to the hydrogenation of CO2 into various C1 products HCOOH, H2CO, and CH3OH. Generally, H2 activation is the rate-determining step in the entire CO2 hydrogenation process, the corresponding relatively low free energy barriers range from 14.5 to 15.9 kcal/mol, and the desorption of products on NiAl-deposited NU-1000 is relatively facile. Although the Al atom does not directly participate in the reaction, its presence provides exposed oxygen sites that facilitate the heterolytic cleavage of H2 and the hydrogenation of C1 intermediates, which plays an important role in enhancing the catalytic activity of the Ni site. The present study demonstrates that the catalytic performance of NU-1000 can be finely tuned by depositing heterometal-oxo clusters, and the porous MOF should be an attractive platform for the construction of atomically dispersed catalysts.

Elucidating the degradation mechanism of the nerve agent A-234 using various detergents: a theoretical investigation.

A-234 (ethyl N-[1-(diethylamino)ethylidene]phosphoramidofluoridate) is one of the highly toxic Novichok nerve agents, and its efficient degradation is of significant importance. The possible degradation mechanisms of A-234 by H2O, H2O2, NH3, and their combinations have been extensively investigated by using density functional theory (DFT) calculations. According to the initial intermolecular interaction and the proton transfer patterns between the detergent and the substrate A-234, the A-234 degradation reaction is classified into three categories, denoted as A, B, and C. In modes A and B, the degradation of A-234 by H2O2, H2O, and NH3 is initiated by the nucleophilic attack of the O or N atom of the detergent on the P atom of A-234, coupled with the proton transfer from the detergent to the O or N atom of A-234, whereas in mode C, the direct interaction of H2N-H with the F-P bond of A-234 triggers ammonolysis through a one-step mechanism with the formation of H-F and N-P bonds. Perhydrolysis and hydrolysis of A-234 can be remarkably promoted by introducing the auxiliary NH3, and the timely formed hydrogen bond network among detergent, auxiliary, and substrate molecules is responsible for the enhancement of degradation efficiency.

Narrowband emission from fully-bridged triphenylamine derivatives: insights into effects of structure modification and pressure.

Triphenylamine derivatives with narrowband emission have attracted growing attention in purely organic thermally-activated fluorescence (TADF) materials owing to their enhanced color purity and flexible molecular design strategy. Combined time-dependent density functional theory (TD-DFT) and ONIOM (QM/MM) calculations indicate that the excellent planarity of the experimentally developed DQAO could result in gradually decreased intermolecular interactions in the aggregated state at ambient pressure and upon compression, which is unfavorable for suppressing structural relaxation and achieving narrowband emission in its non-doped practical application. Therefore, three structure-modified derivatives, DQAO-Cb, DQAO-Ph, and DQAO-PhCb, were theoretically designed by introducing the spherical o-carborane and dangling phenyl units positioned para to the N atom of the DQAO to provide additional geometrical distortion and steric hindrance. The explorations on the reported DQAO, OQAO, and SQAO found that small structural relaxations, suppressed low-frequency vibrations, and noticeable short-range charge-transfer (SR-CT) natures of DQAO and OQAO are responsible for their much narrower emission spectral full-width at half-maxima (FWHMs) compared to that of SQAO. Introducing the o-carborane unit directly at the para position of the N atom could result in additional scissoring and stretching vibrations of the corresponding DQAO-Cb while the presence of the phenyl unit in DQAO-Ph is beneficial for suppressing the high-frequency vibrations of the pristine DQAO. More importantly, the bridged phenyl unit incorporated in DQAO-PhCb is of particular importance to inhibit the undesired low-frequency scissoring and high-frequency stretching vibrations of the o-carborane unit, which is crucial to reduce the reorganization energy of DQAO-PhCb and achieve narrowband emission. Also, the phenyl unit in DQAO-Ph and DQAO-PhCb helps to shorten charge transfer distances and improve ISC and RISC processes. Since the o-carborane unit is an adopted building block to achieve piezochromic behaviors, the theoretically structure-modified DQAO-PhCb is expected to exhibit narrowband emission, TADF, and piezochromic features all together. Our findings will hopefully provide ideas for designing triphenylamine-based TADF emitters with narrowband emission and piezochromic behaviors.

THF-Assisted CO2 Reduction Catalyzed by Electride Mg2EP: Insight from DFT Calculations.

Hydroboration and hydrogenation reductions of CO2 catalyzed by a porphyrinoid-based dimagnesium(I) electride (Mg2EP) were investigated by density functional theory calculations. Herein, the presence of potentially excess electrons located at the Mg-Mg bond endows Mg2EP with the ability to activate small molecules such as CO2, HBpin, and H2, thus opening up the possibility for further CO2 conversion. The Mg2EP-catalyzed hydroboration of CO2 to HCOOBpin is predicted to have relatively higher activity in comparison to the hydrogenation reduction to formic acid (HCOOH). Interestingly, the common solvent molecule tetrahydrofuran as an auxiliary can coordinate with the Mg center to effectively weaken the bonding interaction between the dimagnesium center and the intermediate species from the CO2 conversion, thereby promoting the catalytic cycle for the CO2 hydroboration. The present results suggest that the electride Mg2EP is promising for the molecular catalyst in the CO2 transformation.

How the Conformational Movement of the Substrate Drives the Regioselective C-N Bond Formation in P450 TleB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations.

P450 TleB catalyzes the oxidative cyclization of the dipeptide N-methylvalyl-tryptophanol into indolactam V through selective intramolecular C-H bond amination at the indole C4 position. Understanding its catalytic mechanism is instrumental for the engineering or design of P450-catalyzed C-H amination reactions. Using multiscale computational methods, we show that the reaction proceeds through a diradical pathway, involving a hydrogen atom transfer (HAT) from N1-H to Cpd I, a conformational transformation of the substrate radical species, and a second HAT from N13-H to Cpd II. Intriguingly, the conformational transformation is found to be the key to enabling efficient and selective C-N coupling between N13 and C4 in the subsequent diradical coupling reaction. The underlined conformational transformation is triggered by the first HAT, which proceeds with an energy-demanding indole ring flip and is followed by the facile approach of the N13-H group to Cpd II. Detailed analysis shows that the internal electric field (IEF) from the protein environment plays key roles in the transformation process, which not only provides the driving force but also stabilizes the flipped conformation of the indole radical. Our simulations provide a clear picture of how the P450 enzyme can smartly modulate the selective C-N coupling reaction. The present findings are in line with all available experimental data, highlighting the crucial role of substrate dynamics in controlling this highly valuable reaction.

Formation and reactivity of NHC-boryl radicals: insight into substituent effect from theoretical calculations.

Substituent modification effects of N-heterocyclic carbene (NHC) boranes on their hydrogen atom abstraction (HAA) reactions and the chemical reactivities of corresponding NHC-boryl radicals have been investigated by density functional theory calculations. The substituent modification of NHC-boranes may notably affect the HAA reaction, both kinetically and thermodynamically, and shows remarkable substitution position dependence. The multi-site-modification of NHC-boranes is proved to be more effective for reduction of the B-H bond dissociation energy (BDE), promotion of the HAA reaction, and the reactivity regulation of their corresponding NHC-boryl radicals. Computational screening reveals that the spin density and the charge population of the radical boron center have good correlation with the B-H BDEs of NHC-boranes and the chemical reactivities of NHC-boryl radicals, and they can be considered as property and reactivity descriptors of these boron-based systems. The present results and established scaling relationships are beneficial to promote the advancement of design of NHC-boryl radical catalysis.

Biodegradation of 2,5-Dihydroxypyridine by 2,5-Dihydroxypyridine Dioxygenase and Its Mutants: Insights into O-O Bond Activation and Flexible Reaction Mechanisms from QM/MM Simulations.

2,5-Dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440 is a mononuclear non-heme iron oxygenase responsible for the biodegradation of 2,5-dihydroxypyridine (DHP) to N-formylmaleamic acid (NFM). Here, extensive quantum mechanical-molecular mechanical (QM/MM) calculations and molecular dynamics (MD) simulations are used to elucidate the degradation mechanism of DHP by wild-type NicX and its H105F variant (NicXH105F) and the roles of key residues. In particular, NicX and NicXH105F can catalyze the ring opening degradation of DHP to NFM, but flexible mechanisms are adopted therein. Both reactions of NicX and NicXH105F are initiated by the attack of FeIII superoxide species onto the substrate, during which a proton-coupled electron transfer (PCET) process is involved. For wild-type NicX, the PCET reaction is mediated by the adjacent His105, while the further proton transfer from His105 to the peroxo species can remarkably enhance the following O-O cleavage. However, for the NicXH105F mutant, a water molecule replaces the role of residue His105, which not only stabilizes the substrate binding via a H bonding network but also functions as a base to mediate the PCET process. For the NicXH105A mutant, MD simulations show that the disruption of the H bonding network can displace the substrate binding, leading to the loss of enzyme activity. These findings can expand our understanding of the PCET-mediated O-O bond activation and the flexible catalytic routes in various mutants, which have general implications on enzyme catalysis.

Hydroboration of CO2 to Methyl Boronate Catalyzed by a Manganese Pincer Complex: Insights into the Reaction Mechanism and Ligand Effect.

The conversion of carbon dioxide to fuels, polymers, and chemicals is an attractive strategy for the synthesis of high-value-added products and energy-storage materials. Herein, the density functional theory method was employed to investigate the reaction mechanism of CO2 hydroboration catalyzed by manganese pincer complex, [Mn(Ph2PCH2SiMe2)2NH(CO)2Br]. The carbonyl association and carbonyl dissociation mechanisms were investigated, and the calculated results showed that the carbonyl association mechanism is more favorable with an energetic span of 27.0 kcal/mol. Meanwhile, the solvent effect of the reaction was explored, indicating that the solvents could reduce the catalytic activity of the catalyst, which was consistent with the experimental results. In addition, the X ligand effect (X = CO, Br, H, PH3) on the catalytic activity of the manganese complex was explored, indicating that the anionic complexes [MnI - Br]- and [MnI - H]- have higher catalytic activity. This may not only shed light on the fixation and conversion of CO2 catalyzed by earth-abundant transition-metal complexes but also provide theoretical insights to design new transition-metal catalysts.

RBD spatial orientation of the spike protein and its binding to ACE2: insight into the high infectivity of the SARS-CoV-2 Delta variant from MD simulations.

The spike glycoprotein on the surface of the SARS-CoV-2 envelope plays an important role in its invasion into host cells. The binding of the spike glycoprotein RBD to the angiotensin-converting enzyme 2 (ACE2) receptor as a critical step in the spread of the virus has been explored intensively since the outbreak of COVID-19, but the high transmissibility of the virus such as the Delta variant is still not fully understood. Here, molecular simulations on the binding interactions of the wild-type spike protein and its four variants (Beta, Kappa, Delta, and Mu) with ACE2 and the antibody were performed, and the present results reveal that the residue mutations will not strengthen the binding affinity of the variant for ACE2, but remarkably influences the spatial orientation of the spike protein. Only the up-right conformational receptor binding domain (RBD) can bind ACE2, which is stabilized by the nearby RBDs in the down state, revealing that the RBD bears dual functional characteristics. The present results provide new insights into plausible mechanisms for high infectivity of the virus variants and their immune escape.

Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations.

Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Znα-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.

QM/MM and MM MD simulations on decontamination of the V-type nerve agent VX by phosphotriesterase: toward a comprehensive understanding of steroselectivity and activity.

Due to deadly toxicity and high environmental stability of the nerve agent VX, an efficient decontamination approach is desperately needed in tackling its severe threat to human security. The enzymatic destruction of nerve agents has been generally considered as one of the most effective ways, and here the hydrolysis of VX by phosphotriesterase (PTE) was investigated by extensive QM/MM and MM MD simulations. The hydrolytic cleavage of P-S by PTE is a two-step process with the free energy spans of 15.8 and 26.0 kcal mol-1 for the RP- and SP-enantiomer VX, respectively, and such remarkable stereospecificity of VX enantiomers in the enzymatic degradation is attributed to their conformational compatibility with the active pocket. The structurally less adaptive SP-enantiomer allows one additional water molecule to enter the binuclear zinc center and remarkably facilitates the release of the degraded product. Overall, the rate-limiting steps in the enzymatic degradation of VX by PTE involve the degraded product release of the RP-enantiomer and the enzymatic P-S cleavage of the SP-enantiomer. Further computational analysis on the mutation of selected residues also revealed that H257Y, H257D, H254Q-H257F, and L7ep-3a variants allow more water molecules to enter the active site, which improves the catalytic efficiency of PTE, as observed experimentally. The present work provides mechanistic insights into the stereoselective hydrolysis of VX by PTE and the activity manipulation through the active-site accessibility of water molecules, which can be used for the enzyme engineering to defeat chemical warfare agents.

Planar Tetracoordinate Silicon in Organic Molecules As Carbenoid-Type Amphoteric Centers: A Computational Study.

Designing and synthesizing a stable compound with a planar tetracoordinate silicon (ptSi) center is a challenging goal for chemists. Here, a series of potential aromatic ptSi compounds composed of four conjugated rings shared by a centrally embedded Si atom are theoretically designed and computationally verified. Both Born-Oppenheimer molecular dynamics (BOMD) simulations and potential energy surface scannings verify the high stability and likely existence of these compounds, particularly Si-16-5555 (SiN4 C8 H8 ) with 16 π electrons, under standard ambient temperature and pressure. Notably, the Hückel aromaticity rule, which works well for single rings, is inconsistent with the high stability of Si-16-5555 where the 16 p electrons are spread over four five-membered rings fused together. Bonding analyses show that the strong electron donation from the peripheral 12-membered conjugated ring with 16 π electrons to the vacant central atomic orbital Si 3pz leads to the stabilization for both the ptSi coordination and planar aromaticity. The partial occupation of Si 3pz results in the peculiar carbenoid-type behaviors for the amphoteric center. By modulating the electron density on the ring with substituent groups, we can regulate the nucleophilic and electrophilic properties of the central Si.

Mechanisms and kinetics of the low-temperature oxidation of 2-methylfuran: insight from DFT calculations and kinetic simulations.

The low-temperature oxidation (LTO) mechanisms of the 2-methylfuran (2-MF) biofuel and the corresponding thermodynamic and kinetic properties have been explored by density functional theory (DFT) and composite G4 methodologies as well as kinetic simulations. The O2 addition to the main furylCH2 radical from the methyl dehydrogenation in 2-MF forms three peroxide radicals PO1, PO2, and PO3 with the energy barriers of 15.1, 19.3, and 20.6 kcal mol-1 and the reaction ΔG of -8.2, 5.7, and -0.1 kcal mol-1 (298 K and 1 atm), respectively. Through hydrogen transfer followed by dehydroxylation, these nascent products evolve into stable aldehydes and cyclic ketones, which may further decompose into smaller species under the action of OH. Calculations and simulations show that the product P1 from the dehydroxylation of PO1 has a dominant population (higher than 96%) among the final products, although the temperature and pressure may influence the species profiles and rate constants to some extent. Based on the G4-calibrated thermodynamic parameters, the temperature and pressure dependence of the rate constants and the two- and three-parameter Arrhenius coefficients for all reactions considered here have been determined by using the transition state theory (TST) and Rice-Ramsperger-Kassel-Marcus (RRKM) methods. The present results provide a comprehensive understanding of the mechanisms and kinetics of the LTO process of the 2-MF biofuel.

Oxygen migration and optical properties of coronene oxides and their persulfurated derivatives: insight into the electric field effect and the oxygen-site dependence.

Oxygen migration and spectroscopic properties of coronene (C24) epoxides and persulfurated coronene (PSC) oxides have been investigated by using density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The rim-oxide is predicted to be more energetically favorable than the oxygen-centered configuration, and the application of an external electric field can accelerate the epoxy migration from the middle to the edge of the molecule. The predicted electronic absorptions and emissions of the C24 epoxides strongly depend on the location of oxygen. In particular, the stable edge-epoxide C24d3 has the largest radiative decay rate (kr) and the smallest non-radiative decay rate (knr), suggesting relatively strong fluorescence emission. On the contrary, absorptions and emissions of the PSC oxides are less changed, compared to those of the pristine PSC. On-the-fly trajectory surface hopping dynamics simulations reveal that the nonadiabatic S1 → S0 decay of the C24 epoxides is triggered by C-O bond stretching, and thus the radiative and nonradiative features depend on the C-O bond strength. The present results indicate that the oxygen diffusion on the basal plane of graphene oxides is easily tuned by the external electric field and their optoelectronic properties show a notable oxygen-site dependence.

QM/MM MD simulations reveal an asynchronous PCET mechanism for nitrite reduction by copper nitrite reductase.

Nitrite reductases are enzymes that aid in the denitrification process by catalyzing the reduction of nitrite to nitric oxide gas. Since this reaction is the first committed step that involves gas formation, it is regarded to be a vital step for denitrification. However, the mechanism of copper-containing nitrite reductase is still under debate due to the discrepancy between the theoretical and experimental data, especially in terms of the roles of secondary shell residues Asp98 and His255 and the electron transfer mechanism between the two copper sites. Herein, we revisited the nitrite reduction mechanism of A. faecalis copper nitrite reductase using QM(B3LYP)/MM-based metadynamics. It is found that the intramolecular electron transfer from T1-Cu to T2-Cu occurs via an asynchronous proton-coupled electron transfer (PCET) mechanism, with electron transfer (ET) preceding proton transfer (PT). In particular, we found that the ET process is driven by the conformation conversion of Asp98 from the gatekeeper to the proximal one, which is much more energy-demanding than the PCET itself. These results highlight that the inclusion of an electron donor is vital to investigate electron-transfer related processes such as PCET.

Fenton-Derived OH Radicals Enable the MPnS Enzyme to Convert 2-Hydroxyethylphosphonate to Methylphosphonate: Insights from Ab Initio QM/MM MD Simulations.

The mechanism for dioxygen activation represents one of the core issues in metalloenzymes. In most cases, the activation of the O2 molecule requires additional electrons from an external reducant. However, nonheme hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are exceptional C-H oxygenases. Both enzymes do not utilize reductants, rather they employ directly iron(III)-superoxide species to initiate H-abstraction reactions and lead thereby to catalysis of the C-C cleavage in 2-hydroxyethylphosphonate (2-HEP). Using the recently characterized MPnS structure and QM(B3LYP)/MM-based metadynamics simulations, we deciphered the chemical mechanism for MPnS. Our simulations demonstrate O2 activation in MPnS is mediated by an adjacent Lysine residue (Lys28) in the active site, leading to an unusual H 2 O 2 intermediate in the reductant-independent nonheme MPnS enzyme. Furthermore, the so-generated H 2 O 2 intermediate is subsequently employed in a Fenton-type reaction, leading to a locked •OH radical that spontaneously attaches to the substrate carbonyl group. Meanwhile, the proton from the Fe(III)-OH is shuttled back to the deprotonated Lys28, affording the Fe(IV)-oxo species that is identified by experiment in HEPD. Thus, our calculations demonstrate an unusual proton-shuttle mechanism for O 2 activation in metalloenzymes.

Theory Demonstrated a "Coupled" Mechanism for O2 Activation and Substrate Hydroxylation by Binuclear Copper Monooxygenases.

Multiscale simulations have been performed to address the longstanding issue of "dioxygen activation" by the binuclear copper monooxygenases (PHM and DßM), which have been traditionally classified as "noncoupled" binuclear copper enzymes. Our QM/MM calculations rule out that CuM(II)-O2• is an active species for H-abstraction from the substrate. In contrast, CuM(II)-O2• would abstract an H atom from the cosubstrate ascorbate to form a CuM(II)-OOH intermediate in PHM and DßM. Consistent with the recently reported structural features of DßM, the umbrella sampling shows that the "open" conformation of the CuM(II)-OOH intermediate could readily transform into the "closed" conformation in PHM, in which we located a mixed-valent µ-hydroperoxodicopper(I,II) intermediate, (µ-OOH)Cu(I)Cu(II). The subsequent O-O cleavage and OH moiety migration to CuH generate the unexpected species (µ-O•)(µ-OH)Cu(II)Cu(II), which is revealed to be the reactive intermediate responsible for substrate hydroxylation. We also demonstrate that the flexible Met ligand is favorable for O-O cleavage reactions, while the replacement of Met with the strongly bound His ligand would inhibit the O-O cleavage reactivity. As such, the study not only demonstrates a "coupled" mechanism for O2 activation by binuclear copper monooxygenases but also deciphers the full catalytic cycle of PHM and DßM in accord with the available experimental data. These findings of O2 activation and substrate hydroxylation by binuclear copper monooxygenases could expand our understanding of the reactivities of the synthetic monocopper complexes.

Computational insight into excited states of the ring-opening radicals from the pyrolysis of furan biofuels.

The low-lying valence excited states and Rydberg states of the radical species from the ring-opening reactions in pyrolysis of furan biofuels have been determined by extensive density functional theory and sophisticated wave function theory calculations. The radicals 1-C4 H5 O-2, 2-furylCH2 , and 4-C6 H7 O with the delocalized π-type single electron are predicted to be most stable among the reactive species here for furan, 2-methyfuran, and 2,5-dimethylfuran, respectively. Predicted vertical transition energies by TD-CAM-B3LYP show good agreement with those by CASPT2. Some among the electronic excitations to low-lying states can take place in the visible light region, and they may be involved in the combustion process. Further surface hopping dynamics simulations on the excited states of the most stable ring-opening radical 1-C4 H5 O-2 of furan as an example reveal that 89.9% sampling trajectories at the initial excited state of 22 A"(π1 π*2 ) decay to the 12 A'(n1 π*2 ) state within an average of 384 fs, and then 81.2% trajectories at the 12 A' state go to the ground state within an average of 114 fs. At the end of the simulation for 1000 fs, 18.8% trajectories still stay on the excited states of 22 A" and 12 A', suggesting that the reactive radicals in the ground state are mainly responsible for the combustion chemistry of furan biofuels. © 2018 Wiley Periodicals, Inc.

Insight into the delivery channel and selectivity of multiple binding sites in bovine serum albumin towards naphthalimide-polyamine derivatives.

Naphthalimide derivatives are types of small-molecule anticancer drug candidates; however, their negative factors and potential side effects make their application limited. The pharmacophores select a direct access into the tumor cells as the first choice; this can reduce the side effect of the anti-cancer drugs on the normal cells. Herein, the delivery and binding of the naphthalimide-polyamine complex assisted by the bovine serum albumin (BSA) protein have been studied by combining several molecular dynamic simulations. The plausible transportation channels and the most favorable pathways for the delivery of the naphthalimide-polyamine complex to two drug sites (DSI and DSII), their thermodynamic and dynamic properties and the mechanisms have been discussed in detail. The residues His287 and Phe394 acted as guards in the DSI and DSII, respectively, which played a gating-switch role by flipping the ring from open to close during the compound delivery. The binding mode, binding energy and substituent effects have been also identified. The two drug sites have different preferences towards the compound with the electron-withdrawing and electron-donating substituents, and their strong interactions are more sensitive to the number of the substituent groups. The naphthalimide-polyamine complexes are more likely to choose DSI, both thermodynamically and dynamically, as compared to DSII. This selective specificity of these two drug sites manipulated by the electron-withdrawing and electron-donating substituents is quite promising for the design of new naphthalimide drugs.

A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data.

The rapid development of cryo-electron microscopy (cryo-EM) has led to the generation of significant low-resolution electron density data of biomolecules. However, the atomistic details of huge biomolecules usually cannot be obtained because it is very difficult to construct all-atom models for MD simulations. Thus, it is still a challenge to make use of the rich low-resolution cryo-EM data for computer simulation and functional study. In this study, we proposed a new method called Convolutional and K-means Coarse-Graining (CK-CG) for the efficient coarse-graining of large biological systems. Using the CK-CG method, we could directly map the cryo-EM data into coarse-grained (CG) beads. Furthermore, the CG beads were parameterized with an empirical harmonic potential to construct a new CG model. We subjected the CK-CG models of the fibrillar protein assemblies F-actin and collagen to external forces in pulling dynamic simulations to assess their mechanical response. The agreement between the estimated tensile stiffness between CG models and experiments demonstrates the validity of the CK-CG method. Thus, our method provides a practical strategy for the direct construction of a structural model from low-resolution data for biological function studies.