DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model.

While significant advances have been made in predicting static protein structures, the inherent dynamics of proteins, modulated by ligands, are crucial for understanding protein function and facilitating drug discovery. Traditional docking methods, frequently used in studying protein-ligand interactions, typically treat proteins as rigid. While molecular dynamics simulations can propose appropriate protein conformations, they're computationally demanding due to rare transitions between biologically relevant equilibrium states. In this study, we present DynamicBind, a deep learning method that employs equivariant geometric diffusion networks to construct a smooth energy landscape, promoting efficient transitions between different equilibrium states. DynamicBind accurately recovers ligand-specific conformations from unbound protein structures without the need for holo-structures or extensive sampling. Remarkably, it demonstrates state-of-the-art performance in docking and virtual screening benchmarks. Our experiments reveal that DynamicBind can accommodate a wide range of large protein conformational changes and identify cryptic pockets in unseen protein targets. As a result, DynamicBind shows potential in accelerating the development of small molecules for previously undruggable targets and expanding the horizons of computational drug discovery.

Roles of the Comproportionation Reaction in SO2 Reduction Using Methane for the Flexible Recovery of Elemental Sulfur or Sulfides.

SO2 reduction with CH4 to produce elemental sulfur (S8) or other sulfides is typically challenging due to high energy barriers and catalyst poisoning by SO2. Herein, we report that a comproportionation reaction (CR) induced by H2S recirculating significantly accelerates the reactions, altering reaction pathways and enabling flexible adjustment of the products from S8 to sulfides. Results show that SO2 can be fully reduced to H2S at a lower temperature of 650 °C, compared to the 800 °C required for the direct reduction (DR), effectively eliminating catalyst poisoning. The kinetic rate constant is significantly improved, with CR at 650 °C exhibiting about 3-fold higher value than DR at 750 °C. Additionally, the apparent activation energy decreases from 128 to 37 kJ/mol with H2S, altering the reaction route. This CR resolves the challenges related to robust sulfur-oxygen bond activation and enhances CH4 dissociation. During the process, the well-dispersed lamellar MoS2 crystallites with Co promoters (CoMoS) act as active species. H2S facilitates the comproportionation reaction, reducing SO2 to a nascent sulfur (Sx*). Subsequently, CH4 efficiently activates CoMoS in the absence of SO2, forming H2S. This shifts the mechanism from Mars-van Krevelen (MvK) in DR to sequential Langmuir-Hinshelwood (L-H) and MvK in CR. Additionally, it mitigates sulfation poisoning through this rapid activation reaction pathway. This unique comproportionation reaction provides a novel strategy for efficient sulfur resource utilization.

Evidence for Water Antibonding Orbital Mixing in the Hydrated Electron from Its Oxygen 1s X-ray Absorption Spectrum.

The X-ray absorption spectrum (XAS) of the hydrated electron (e(aq)-) has been simulated using time-dependent density functional theory with a quantum mechanics/molecular mechanics description. A unique XAS peak at 533 eV is observed with an energy and intensity in quantitative agreement with recent time-resolved experiments, allowing its assignment as arising from water O1s transitions to the singly occupied molecular orbital (SOMO) in which the excess electron resides. The transitions acquire oscillator strength due to the SOMO comprising an admixture of a cavity-localized orbital and water 4a1 and 2b2 antibonding orbitals. The mixing of antibonding orbitals has implications for the strength of couplings between e(aq)- and intramolecular modes of water.

Arbitrary active control of the Pancharatnam-Berry phase in a terahertz metasurface.

Active phase-control metasurfaces show outstanding capability in the active manipulation of light propagation, while the previous active phase control methods have many constraints in the cost of simulation or the phase modulation range. In this paper, we design and demonstrate a phase controlled metastructure based on two circular split ring resonators (CSRRs) composed of silicon and Au with different widths, which can continuously achieve an arbitrary Pancharatnam-Berry (PB) phase between -π and π before or after active control. The PB phase of such a metasurface before active control is determined by the rotation angle of the Au-composed CSRR, while the PB phase after active control is determined by the rotation angle of the silicon-composed CSRR. And active control of the PB phase is realized by varying conductivity of silicon under an external optical pump. Based on this metastructure, active control of light deflection, metalens with arbitrary reconfigurable focal points and achromatic metalens under selective frequencies are designed and simulated. Moreover, the experimental results demonstrate that focal spots of metalens can be actively controlled by the optical pump, in accord with the simulated ones. Our metastructure implements a plethora of metasurfaces' active phase modulation and provides applications in active light manipulation.

Free energy change estimation: The Divide and Conquer MBAR method.

In the present study, the Divide and Conquer MBAR (DC-MBAR) method is proposed to predict the free energies based on the data sampled by multi-states simulations. For DC-MBAR method, the overlap between any two alchemical states is calculated first and those with sufficient overlap are defined as the adjacent states. Unlike the traditional MBAR method, which calculates the free energy of each state using all the data at once, DC-MBAR focuses on predicting the free energy changes between adjacent states. To estimate the free energy changes accurately, the other states with overlaps with the two adjacent states bigger than the defined threshold are included in the MBAR equation. At a specific threshold, the free energies predicted by DC-MBAR are very close to those calculated by the traditional MABR method. Furthermore, DC-MBAR scheme can reduce both the computation and memory cost. One important characteristic of DC-MBAR method is linear scaling, which means the CPU time with the change of the number of states is a straight-line relation. As the pair-based calculations are mutually independent and parallelizable, all accessible CPU cores on the HPC cluster could be utilized, which makes DC-MBAR strategy more efficient.

Solvation Free Energy Calculations: The Combination between the Implicitly Polarized Fixed-charge Model and the Reference Potential Strategy.

The IPolQ-Mod charges, which are the average of two charge sets fitted in vacuum state and condensed phase, take account of polarization effect implicitly in the solvation free energy calculation. However, the performance of the IPolQ-Mod charges sensitively depends on the QM levels used to generate the electrostatic potential from which the charges are fitted. In addition, the forces on atoms are not accurate theoretically in the molecular dynamics (MD) simulation as the solvent only feels the electrostatic potential of a half-polarized density of the solute according to the derivation of the IPolQ-Mod charges. To study these issues in detail, the IPolQ-Mod charges are combined with the reference potential (RP) strategy to predict the solvation free energies in the present study. It is found that the thermodynamic perturbation (TP) corrections utilizing total energy difference and interaction energy difference are almost the same and free of bias. The solvation free energies estimated by the RP method match very well with those obtained by applying IPolQ-Mod charges into MD simulation directly. By means of the RP strategy, the performances of the IPolQ-Mod charges with the change of the strength of the exact HF exchange in several DFT functionals are determined effectively. Although the "optimal" strengths are found in B3LYP and LC-ωPBE, the improvements over the default strength are not too much. In addition to the IPolQ-Mod charges, other charge models like bond charge correction (BCC) charges could also be combined with the RP strategy to study the thermodynamic properties like solvation free energy. © 2019 Wiley Periodicals, Inc.

Solvation Free Energy Calculation Using a Fixed-Charge Model: Implicit and Explicit Treatments of the Polarization Effect.

In this work, IPolQ-Mod charges and the reference potential scheme are used to calculate the solvation free energies of a set of organic molecules. Both methods could capture the phase transfer of a solute with accompanying polarization cost utilizing a fixed-charge model. The IPolQ-Mod charges, which are the average of two charge sets fitted in a vacuum state and a condensed phase, take account of the polarization effect implicitly. For the reference potential method, the quantum mechanics polarization corrections are calculated explicitly by thermodynamic perturbation. The polarization effect captured by the IPolQ-Mod charges is an approximation to that of the reference potential method theoretically. In the present study, the reference potential method shows a slight improvement over the classical restrained electrostatic potential (RESP) charges, which perform pretty well in predicting the solvation free energy. However, IPolQ-Mod(MP2) shows a poor agreement with the experimental data. Compared with IPolQ-Mod(MP2), IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) is found to give more appropriate prediction of the molecule's dipole and the solvation free energies calculated by IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) are more compatible with those of the RESP charges. If the other force field parameters remain unchanged, M06-2X or ωB97X is recommended to derive the IPolQ-Mod charges.

Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation.

Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at the ab initio (ai) quantum mechanical/molecular mechanics (QM/MM) level is still far too expensive. Although semiempirical (SE) method can be hundreds or thousands of times faster than the ai methods, the accuracy of SE methods is often unsatisfactory due to the approximations that have been adopted in these methods. In this work, we propose a new method termed MBAR+wTP in which the ai QM/MM free energy profile is computed by a weighted thermodynamic perturbation (TP) correction to the SE profile generated by the multistate Bennett acceptance ratio (MBAR) analysis of the trajectories from umbrella samplings (US). The weight factors used in the TP calculations are a byproduct of the MBAR analysis in the postprocessing of the US trajectories, which are often discarded after the free energy calculations. The raw ai QM/MM free energy profile is then smoothed using Gaussian process regression in which the noise of each datum is set to be inversely proportional to the exponential of the reweighting entropy. The results show that this approach can enhance the efficiency of ai FE profile calculations by several orders of magnitude with only a slight loss of accuracy. This method can significantly enhance the applicability of ai QM/MM methods in the studies of chemical reactions in condensed phase and enzymatic reactions.

Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level.

For Diels⁻Alder (DA) reactions in solution, an accurate and converged free energy (FE) surface at ab initio (ai) quantum mechanical/molecular mechanical (QM/MM) level is imperative for the understanding of reaction mechanism. However, this computation is still far too expensive. In a previous work, we proposed a new method termed MBAR+wTP, with which the computation of the ai FE profile can be accelerated by several orders of magnitude via a three-step procedure: (I) an umbrella sampling (US) using a semi-empirical (SE) QM/MM Hamiltonian is performed; (II) the FE profile is generated using the Multistate Bennett Acceptance Ratio (MBAR) analysis; and (III) a weighted Thermodynamic Perturbation (wTP) from the SE Hamiltonian to the ai Hamiltonian is performed to obtain the ai QM/MM FE profile using weight factors from the MBAR analysis. In this work, this method is extended to the calculations of two-dimensional FE surfaces of two Diels⁻Alder reactions of cyclopentadiene with either acrylonitrile or 1-4-naphthoquinone at ai QM/MM level. The accurate activation free energies at the ai QM/MM level, which are much closer to the experimental measurements than those calculated by other methods, indicate that this MBAR+wTP method can be applied in the studies of complex reactions in condensed phase with much-enhanced efficiency.

Combination of a graphene SERS substrate and magnetic solid phase micro-extraction used for the rapid detection of trace illegal additives.

Surface enhanced Raman scattering (SERS) is an ultra-sensitive spectroscopy technique, which can provide rich structural information for a great number of molecules, while solid phase micro-extraction (SPME) is an efficient method for sample pretreatment in analytical chemistry, particularly in a micro-system. In the present report, a silver-loaded and graphene-based magnetic composite (Fe3O4@GO@Ag) was fabricated for use as both a SERS-active substrate and SPME material. The π-π stacking and fluorescence quenching abilities of GO make the composite a perfect candidate for SERS in analyzing real-world samples. Therefore, through combining the magnetic nanoparticles with a SPME device, we have developed a pretreatment method named as disperse magnetic solid phase micro-extraction (Dis-MSPME). In comparison to traditional SPME, the proposed Dis-MSPME realized solid phase micro-extraction from a dispersive system and largely improved the extraction efficiency. Furthermore, by combining the advantages of both Dis-MSPME and SERS we have proposed a new detection method called Dis-MSPME-SERS. Finally, as an example, the illegal additive chloramphenicol (CAP) was successfully detected in aqueous solution with low LOQ and LOD values (1.0 × 10-8 and 1.0 × 10-10 M, respectively), which was finalized within 10 min based on the proposed Dis-MSPME-SERS method. Therefore, a simpler, more efficient and sensitive approach to realize enrichment, magnetic separation and detection, all-in-one, for the detection of illegal additives has been reported, which will be promising towards the detection of trace amounts of substance in micro-systems.

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level.

The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics (MM) rather difficult. In contrast, quantum mechanics (QM) can provide more reliable predictions. In this work, the partition coefficients of the side chain analogs of some amino acids between water and chloroform were computed. The QM solvation free energies were calculated indirectly via a series of MM states using the multistate Bennett acceptance ratio (MBAR) and the MM-to-QM corrections were applied at the two endpoints using thermodynamic perturbation (TP). Previously, it has been shown (Jia et al. J. Chem. Theory Comput. 2016, 12, 499-511) that this method provides the minimal variance in the results without running QM simulations. However, if there is insufficient overlap in phase space between the MM and QM Hamiltonians, this method fails. In this work, we propose, for the first time, a quantity termed the reweighting entropy that serves as a metric for the reliability of the TP calculations. If the reweighting entropy is below a certain threshold (0.65 for the solvation free energy calculations in this work), this MM-to-QM correction should be avoided and two alternative methods can be employed by either introducing a semiempirical state or conducting nonequilibrium simulations. However, the results show that the QM methods are not guaranteed to yield better results than the MM methods. Further improvement of the QM methods are imperative, especially the treatment of the van der Waals and the electrostatic interactions between the QM region and the MM region in the first shell. We also propose a scheme for the calculation of the van der Waals parameters for the solute molecules in nonaqueous solvent, which improves the quality of the computed thermodynamic properties. Furthermore, the force field parameters for the sulfur-containing molecules are also optimized.

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.

Iminopyridine-Based Cobalt(II) and Nickel(II) Complexes: Synthesis, Characterization, and Their Catalytic Behaviors for 1,3-Butadiene Polymerization.

A series of iminopyridine ligated Co(II) (1a⁻7a) and Ni(II) (1b⁻7b) complexes were synthesized. The structures of complexes 3a, 4a, 5a, 7a, 5b, and 6b were determined by X-ray crystallographic analyses. Complex 3a formed a chloro-bridged dimer, whereas 4a, 5a, and 7a, having a substituent (4a, 5a: CH3; 7a: Br) at the 6-position of pyridine, producing the solid structures with a single ligand coordinated to the central metal. The nickel atom in complex 5b features distorted trigonal-bipyramidal geometry with one THF molecule ligating to the metal center. All the complexes activated by ethylaluminum sesquichloride (EASC) were evaluated in 1,3-butadiene polymerization. The catalytic activity and selectivity were significantly influenced by the ligand structure and central metal. Comparing with the nickel complexes, the cobalt complexes exhibited higher catalytic activity and cis-1,4-selectivity. For both the cobalt and nickel complexes, the aldimine-based complexes showed higher catalyst activity than their ketimine counterparts.

Hybrid QM/MM study of FMO complex with polarized protein-specific charge.

The Fenna-Matthews-Olson (FMO) light-harvesting complex is now one of the primary model systems for the study of excitation energy transfer (EET). However, the mechanism of the EET in this system is still controversial. In this work, molecular dynamics simulations and the electrostatic-embedding quantum-mechanics/molecular-mechanics single-point calculations have been employed to predict the energy transfer pathways utilizing the polarized protein-specific charge (PPC), which provides a more realistic description of Coulomb interaction potential in the protein than conventional mean-field charge scheme. The recently discovered eighth pigment has also been included in this study. Comparing with the conventional mean-field charges, more stable structures of FMO complex were found under PPC scheme during molecular dynamic simulation. Based on the electronic structure calculations, an exciton model was constructed to consider the couplings during excitation. The results show that pigments 3 and 4 dominate the lowest exciton levels whereas the highest exciton level are mainly constituted of pigments 1 and 6. This observation agrees well with the assumption based on the spatial distribution of the pigments. Moreover, the obtained spectral density in this study gives a reliable description of the diverse local environment embedding each pigment.

Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis.

The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and ß-secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic-potential-based charge fitting methods via a dual-step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design.

An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins.

An efficient approach that combines the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method with conductor-like polarizable continuum model (CPCM), termed EE-GMFCC-CPCM, is developed for ab initio calculation of the electrostatic solvation energy of proteins. Compared with the previous MFCC-CPCM study [Y. Mei, C. G. Ji, and J. Z. H. Zhang, J. Chem. Phys. 125, 094906 (2006)], quantum mechanical (QM) calculation is applied to deal with short-range non-neighboring interactions replacing the classical treatment. Numerical studies are carried out for proteins up to 3837 atoms at the HF/6-31G* level. As compared to standard full system CPCM calculations, EE-GMFCC-CPCM shows clear improvement over the MFCC-CPCM method for both the total electrostatic solvation energy and its components (the polarized solute-solvent reaction field energy and wavefunction distortion energy of the solute). For large proteins with 1000-4000 atoms, where the standard full system ab initio CPCM calculations are not affordable, the EE-GMFCC-CPCM gives larger relative wavefunction distortion energies and weaker relative electrostatic solvation energies for proteins, as compared to the corresponding energies calculated by the Divide-and-Conquer Poisson-Boltzmann (D&C-PB) method. Notwithstanding, a high correlation between EE-GMFCC-CPCM and D&C-PB is observed. This study demonstrates that the linear-scaling EE-GMFCC-CPCM approach is an accurate and also efficient method for the calculation of electrostatic solvation energy of proteins.

The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect.

Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000-fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end-state free energy method to calculate the binding free energies of biotin to wild type streptavidin and its F130L mutant. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein-specific charge, the absolute binding affinities are significantly enhanced. In particular, both the absolute and relative binding affinities are in line with the experimental measurements. Further investigation indicates that polarization effect is indispensable in both the generation of structural ensembles and the calculation of interaction energies. This work verifies Baugh's conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation.

Synthesis of bis(N-arylcarboximidoylchloride)pyridine cobalt(II) complexes and their catalytic behavior for 1,3-butadiene polymerization.

A new family of bis(N-arylcarboximidoylchloride)pyridine cobalt(II) complexes with the general formula [2,6-(ArN=CCl)2C5H3N]CoCl2 (Ar = 2,4,6-Me3C6H2, 4a; 2,6-(i)Pr2C6H3, 4b; 2,6-Me2C6H3, 4c; C6H5, 4d; 4-Cl-2,6-Me2C6H2, 4e) and a typical Brookhart-Gibson-type reference complex [2,6-(2,4,6-Me3C6H2N=CMe)2C5H3N]CoCl2 (5a) were synthesized and characterized. Determined by X-ray crystallographic analysis, complexes 4a, 4c-e, and 5a adopted a trigonal bipyramidal configuration, and 4b adopted a distorted square pyramidal geometry. In combination with ethylaluminum sesquichloride (EASC), all the complexes were highly active towards 1,3-butadiene polymerization, affording polybutadiene with predominant cis-1,4 content (up to 96%). 4a with chlorine atoms at the imine groups exhibited higher catalytic activity than did 5a, indicating that the incorporation of chlorine atoms into the ligand improves the activity. The activity of the complexes in 1,3-butadiene polymerization was in the order of 4a > 4c ∼ 4e ∼ 4b > 4d, which is consistent with the trend of spatial opening degree around the metal center in the complexes as revealed by crystallographic data. Screening polymerization conditions proved that EASC was the most efficient among the cocatalysts examined.

Assessing the accuracy of the general AMBER force field for 2,2,2-trifluoroethanol as solvent.

The alcohol-based cosolvent 2,2,2-trifluoroethanol (TFE) has been used widely in protein science and engineering. Many experimental and computational studies of its impact on protein structure have been carried out, but consensus on the mechanism has not been reached. In the past decade, several molecular mechanical models have been proposed to model the structure and dynamics of TFE. However, further calibration is still necessary. In particular, its compatibility with protein force fields has not been well examined. The general AMBER force field (GAFF) has proved quite successful in modeling small organic molecules, and is compatible with contemporary AMBER force field. In this work, we assessed the accuracy of GAFF for the TFE molecule as a bulk solvent. Several properties, such as density, dipole moment, radial distribution function, etc., were calculated and compared with experimental data. The results show that GAFF plays fairly well in the description of bulk TFE, although there is still room for improvement.