Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 24
Filter
1.
Environ Sci Technol ; 58(1): 960-969, 2024 Jan 09.
Article in English | MEDLINE | ID: mdl-38150269

ABSTRACT

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.


Subject(s)
Methane , Sulfur Dioxide , Methane/chemistry , Sulfides/chemistry , Temperature , Sulfur/chemistry , Oxidation-Reduction
2.
Environ Res ; 261: 119705, 2024 Nov 15.
Article in English | MEDLINE | ID: mdl-39084505

ABSTRACT

Long-term biomonitoring of urinary metal ions is an essential tool for the epidemiological assessment of chronic exposure levels, enabling us to track changes in metal exposure over time and better understand its health implications. In this study, we evaluated the temporal trends of urinary metal ions among 1962 residents of Guangzhou, China, from 2018 to 2022. The total metal ion concentrations in the urine of the population did not change significantly between 2018 and 2019. With the onset of the COVID-19 pandemic in 2020, urinary total metal ion concentrations began to decline dramatically, reaching their lowest level in 2021. A rebound in concentrations was observed in 2022, which returned to the initial levels observed in 2018. Urine chromium and cadmium concentrations peaked in 2020, while urinary lead levels were the highest in 2021, and urinary nickel concentrations were the highest in 2022. Males consistently displayed higher urinary concentrations of lead and arsenic throughout each year of the study. Furthermore, minors consistently had higher urinary nickel levels than adults, whereas adults consistently had higher urinary cadmium concentrations than minors. Cluster analyses were conducted annually on urinary metal ions to examine the differences in their distribution and to evaluate changes in metal exposure patterns over time. The Monte Carlo simulations indicate that the whole population exhibits a high non-carcinogenic risk from arsenic exposure and significant carcinogenic risks associated with exposure to nickel, arsenic, chromium, and cadmium. The next two years were predicted by a gray prediction model, and the results are tested using mean absolute percentage error which demonstrating high accuracy.


Subject(s)
COVID-19 , Humans , China/epidemiology , COVID-19/epidemiology , Male , Adult , Female , Child , Young Adult , Adolescent , Middle Aged , Environmental Exposure/analysis , Metals/urine , SARS-CoV-2 , Child, Preschool , Risk Assessment , Cadmium/urine , Biological Monitoring
3.
J Sep Sci ; 47(21): e70010, 2024 Nov.
Article in English | MEDLINE | ID: mdl-39494746

ABSTRACT

This study aims to develop and validate a robust analytical method for the quantification of polybrominated diphenyl ethers (PBDEs) in human serum using gas chromatography-tandem mass spectrometry. We compared procedural blanks, recoveries, and operational convenience of liquid-liquid extraction and supported liquid extraction for the determination of serum PBDEs. We evaluated different extraction solvents for their effect on PBDE recoveries. Supported liquid extraction was selected for method validation due to its operational convenience. The method demonstrated satisfactory linearity, sensitivity, and reproducibility, with the range of 0.10-5.00 µg/L for most PBDE congeners and 0.20-10.0 µg/L for PBDE-154 and PBDE-183, with limits of detection ranging from 2 to 48 ng/L, and with matrix effects ranging from 94% to 113%. Quality control assessments indicated that recoveries ranged from 85% to 110% and relative standard deviations of less than 11%. The proposed method was applied to biomonitoring of 111 healthy adults, revealing detectable levels of PBDEs in over 90% of the samples. BDE-47 and BDE-183 were the most prevalent, with mean concentrations of 4.13 and 22.1 ng/L, respectively. Detection frequencies ranged from 0.90% for BDE-17 and BDE-85 to 25.2% for BDE-47. Males had higher mean concentrations of BDE-183 than females.


Subject(s)
Gas Chromatography-Mass Spectrometry , Halogenated Diphenyl Ethers , Liquid-Liquid Extraction , Tandem Mass Spectrometry , Humans , Halogenated Diphenyl Ethers/blood , Tandem Mass Spectrometry/methods , Female , Male , Adult , Gas Chromatography-Mass Spectrometry/methods , Biological Monitoring , Young Adult , Middle Aged
4.
J Am Chem Soc ; 144(43): 19668-19672, 2022 Nov 02.
Article in English | MEDLINE | ID: mdl-36251402

ABSTRACT

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.

5.
Opt Express ; 30(7): 11444-11458, 2022 Mar 28.
Article in English | MEDLINE | ID: mdl-35473088

ABSTRACT

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.

6.
J Comput Chem ; 42(17): 1204-1211, 2021 Jun 30.
Article in English | MEDLINE | ID: mdl-33851438

ABSTRACT

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.

7.
J Comput Chem ; 40(32): 2801-2809, 2019 Dec 15.
Article in English | MEDLINE | ID: mdl-31433076

ABSTRACT

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.

8.
Analyst ; 143(4): 883-890, 2018 Feb 12.
Article in English | MEDLINE | ID: mdl-29345258

ABSTRACT

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.

9.
Molecules ; 23(10)2018 Sep 28.
Article in English | MEDLINE | ID: mdl-30274188

ABSTRACT

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.


Subject(s)
Cycloaddition Reaction , Molecular Dynamics Simulation , Solvents/chemistry , Kinetics , Models, Chemical , Molecular Structure , Quantum Theory , Thermodynamics
10.
J Chem Inf Model ; 57(10): 2476-2489, 2017 10 23.
Article in English | MEDLINE | ID: mdl-28933850

ABSTRACT

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.


Subject(s)
Chloroform/chemistry , Models, Chemical , Quantum Theory , Water/chemistry , Solubility , Solvents , Thermodynamics
11.
J Comput Chem ; 35(9): 737-47, 2014 Apr 05.
Article in English | MEDLINE | ID: mdl-24500844

ABSTRACT

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.


Subject(s)
Proteins/chemistry , Ligands , Protein Conformation , Static Electricity
12.
Chemosphere ; 365: 143353, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39293687

ABSTRACT

Continuous human biomonitoring and predictive modelling of urinary pesticide metabolites are critical for evaluating pesticide exposure trends and associated health risks. We conducted repeat cross-sectional surveys to determine the urinary concentrations of eight pesticide metabolites in the residents of Guangzhou, China, from 2018 to 2022. We longitudinally analyzed the changes in these metabolite concentrations over the years and assessed the potential non-carcinogenic risks by calculating the hazard quotient and hazard index. No significant differences were observed in the total urinary pesticide metabolite concentrations over the 5 years (9.16-12.99 µg/L). The urinary concentrations of 3,5,6-trichloro-2-pyridinol and 2,4-dichlorophenoxyacetic acid reached their lowest levels in 2020 (1.47 and 0.11 µg/L). Conversely, urinary para-nitrophenol concentrations exhibited an inverse trend, peaking in 2020 (6.16 µg/L). The composition profiles of urinary pesticide metabolites showed that para-nitrophenol consistently constituted the largest proportion each year. Males consistently showed higher median concentrations of total urinary pesticide metabolites and individual metabolites of 3,5,6-trichloro-2-pyridinol, trans-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane-1-carboxylic acid, and para-nitrophenol than females. The concentrations of cis-3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropane-1-carboxylic acid in adults' urine were significantly higher than those in minors' urine each year. The total pesticide metabolite concentrations in adults' urine were significantly higher than those in minors' urine in 2018 and 2020, whereas no significant differences were observed in other years. No significant differences in urinary pesticide metabolite concentrations were observed among different BMI groups. Results showed that 14.17% of the population had hazard index values above 1, indicating a higher risk of health hazards. Three predictive models were employed to predict urinary pesticide metabolite concentrations for 2023-2024, revealing an increasing trend in 3,5,6-trichloro-2-pyridinol concentrations while other metabolites are expected to decrease. The study showed the concentration of para-nitrophenol peaked in 2020 while 3,5,6-trichloro-2-pyridinol and 2,4-dichlorophenoxyacetic acid reached their lowest levels, suggests that the COVID-19 pandemic may have influenced pesticide exposure patterns.


Subject(s)
Environmental Exposure , Pesticides , Humans , China , Pesticides/urine , Pesticides/metabolism , Male , Female , Longitudinal Studies , Adult , Middle Aged , Environmental Exposure/statistics & numerical data , Biological Monitoring , Young Adult , Cross-Sectional Studies , 2,4-Dichlorophenoxyacetic Acid/urine , Adolescent , Pyridones/urine , Nitrophenols/urine , Nitrophenols/metabolism , Environmental Pollutants/urine , Environmental Pollutants/metabolism , Environmental Monitoring/methods
13.
ACS Med Chem Lett ; 15(10): 1778-1786, 2024 Oct 10.
Article in English | MEDLINE | ID: mdl-39411524

ABSTRACT

A novel class of kinesin KIF18A inhibitors were discovered through modification of the clinical compound AMG650. Structure-activity relationship (SAR) study led to the discovery of compound 16 with an alkenyl motif, a highly potent KIF18A inhibitor, which displayed a favorable pharmacological profile and excellent efficacy in a mouse model of an OVCAR-3 xenograft tumor. Oral administration of 16 can induce a dose-dependent antitumor efficacy in the OVCAR-3 model without significant reduction in body weight. Compound 16 showed potential as a candidate for the clinical treatment of ovarian cancer.

14.
Nat Commun ; 15(1): 1071, 2024 Feb 05.
Article in English | MEDLINE | ID: mdl-38316797

ABSTRACT

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.


Subject(s)
Molecular Dynamics Simulation , Proteins , Ligands , Proteins/metabolism , Protein Conformation , Drug Discovery , Protein Binding , Molecular Docking Simulation
15.
J Mol Model ; 30(7): 224, 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38907749

ABSTRACT

CONTEXT: The thermal decomposition process of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine/hydroxyl-terminated polybutadiene (HMX/HTPB) hybrid explosives and pure HMX explosives at different temperatures (2000 ~ 3500 K) was investigated using the reactive molecular dynamics method. This study aimed to analyze the effect of binders on the thermal decomposition of HMX at the atomic scale and reveal the thermal decomposition mechanism of HMX/HTPB. The results showed that the thermal decomposition process of the HMX molecule in the HMX/HTPB hybrid system involves a continuous denitration followed by the disintegration of the main ring. The HTPB chain will experience dehydrogenation, dehydroxylation, and chain fragmentation. Including HTPB in the hybrid system significantly increased the presence of H and OH radicals. These radicals then interacted with HMX and its decomposition products and produced more of the final products H2O and H2 in the HMX/HTPB hybrid system compared to pure HMX. Additionally, it was observed that the HTPB chain fragments attached to the HMX decomposition products prevented the formation of N2 and CO2. Furthermore, the activation energies (Ea) of the initial and intermediate decomposition stages of the HMX/HTPB hybrid system were 98.45 kJ mol-1 and 90.69 kJ mol-1, respectively. The results showed that the activation energies of the HMX/HTPB hybrid system are lower than the pure HMX system in these two stages. Consequently, HTPB will enhance HMX's thermal decomposition and decreased the system's insensitivity to heat stimuli. METHODS: The molecular dynamics simulation of the HMX/HTPB hybrid system was performed using the ReaxFF module in the LAMMPS software, and the ReaxFF/lg force field was used to describe the interatomic interactions as well as the chemical reactions.

16.
J Comput Chem ; 34(31): 2677-86, 2013 Dec 05.
Article in English | MEDLINE | ID: mdl-24000160

ABSTRACT

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.


Subject(s)
Biotin/metabolism , Point Mutation/physiology , Streptavidin/metabolism , Binding Sites/genetics , Models, Molecular , Molecular Dynamics Simulation , Point Mutation/genetics , Protein Binding/genetics , Streptavidin/genetics , Thermodynamics
17.
J Chem Phys ; 139(21): 214104, 2013 Dec 07.
Article in English | MEDLINE | ID: mdl-24320361

ABSTRACT

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.


Subject(s)
Proteins/chemistry , Alanine/chemistry , Molecular Dynamics Simulation , Oligopeptides/chemistry , Quantum Theory , Solvents , Static Electricity
18.
J Phys Chem B ; 123(5): 1139-1148, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30628452

ABSTRACT

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.

19.
J Chem Theory Comput ; 14(11): 5583-5596, 2018 Nov 13.
Article in English | MEDLINE | ID: mdl-30336015

ABSTRACT

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.

20.
Polymers (Basel) ; 8(1)2016 Jan 12.
Article in English | MEDLINE | ID: mdl-30979108

ABSTRACT

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.

SELECTION OF CITATIONS
SEARCH DETAIL