Advanced deep learning methods for molecular property prediction

The prediction of molecular properties is a crucial task in the field of drug discovery.Computational methods that can accurately predict molecular properties can significantly accelerate the drug discovery process and reduce the cost of drug discovery.In recent years,iterative updates in computing hardware and the rise of deep learning have created a new and effective path for molecular property prediction.Deep learning methods can leverage the vast amount of data accumulated over the years in drug discovery and do not require complex feature engineering.in this review,we summarize molecular representations and commonly used datasets in molecular property prediction models and present advanced deep learning methods for molecular property prediction,including state-of-the-art deep learning networks such as graph neural networks and Transformer-based models,as well as state-of-the-art deep learning strategies such as 3D pre-train,contrastive learning,multi-task learning,transfer learning,and meta-learning.We also point out some critical issues such as lack of datasets,low information utilization,and lack of specificity for diseases.

A computational toolbox for molecular property prediction based on quantum mechanics and quantitative structure-property relationship

Chemical industry is always seeking opportunities to efficiently and economically convert raw materials to commodity chemicals and higher value-added chemicalbased products.The life cycles of chemical products involve the procedures of conceptual product designs,experimental investigations,sustainable manufactures through appropriate chemical processes and waste disposals.During these periods,one of the most important keys is the molecular property prediction models associating molecular structures with product properties.In this paper,a framework combining quantum mechanics and quantitative structure-property relationship is established for fast molecular property predictions,such as activity coefficient,and so forth.The workflow of framework consists of three steps.In the first step,a database is created for collections of basic molecular information;in the second step,quantum mechanics-based calculations are performed to predict quantum mechanics-based/derived molecular properties(pseudo experimental data),which are stored in a database and further provided for the developments of quantitative structure-property relationship methods for fast predictions of properties in the third step.The whole framework has been carried out within a molecular property prediction toolbox.Two case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction and solid-liquid phase equilibriums are presented.

Interfacial Charge Transfer Induced Electronic Property Tuning of MoS_2 by Molecular Functionalization

The modulation of electrical properties of MoS_2 has attracted extensive research interest because of its potential applications in electronic and optoelectronic devices.Herein,interfacial charge transfer induced electronic property tuning of MoS_2 are investigated by in situ ultraviolet photoelectron spectroscopy and x-ray photoelectron spectroscopy measurements.A downward band-bending of MoS_2-related electronic states along with the decreasing work function,which are induced by the electron transfer from Cs overlayers to MoS_2,is observed after the functionalization of MoS_2 with Cs,leading to n-type doping.Meanwhile,when MoS_2 is modified with 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane(F_4-TCNQ),an upward band-bending of MoS_2-related electronic states along with the increasing work function is observed at the interfaces.This is attributed to the electron depletion within MoS_2 due to the strong electron withdrawing property of F_4-TCNQ,indicating p-type doping of MoS_2.Our findings reveal that surface transfer doping is an effective approach for electronic property tuning of MoS_2 and paves the way to optimize its performance in electronic and optoelectronic devices.

All-electron basis sets for H to Xe specific for ZORA calculations:Applications in atoms and molecules

A segmented basis set of quadruple zeta valence quality plus polarization functions(QZP)for H through Xe was developed to be used in conjunction with the ZORA Hamiltonian.This set was augmented with diffuse functions to describe electrons farther away from the nuclei adequately.Using the ZORA-CCSD(T)/QZP-ZORA theoretical model,atomic ionization energies and bond lengths,harmonic vibrational frequencies,and atomization energies of some molecules were calculated.The addition of core-valence corrections has been shown to improve the agreement between theoretical and experimental results for molecular properties.For atomization energies,a similar observation emerges when considering spin-orbit couplings.With the augmented QZP-ZORA set,static mean dipole polarizabilities of a set of atoms were calculated and compared with previously published recommended and experimental values.Performance evaluations of the ZORA and Douglas–Kroll–Hess Hamiltonians were made for each property studied.

Molecular Properties of 9,10-Phenanthrenequinone and Benzil

9,10-Phenanthrenequinone（PQ） and benzil are important a-diketones. This manuscript explains the first comparison of PQ and benzil molecular properties. We have used 1H NMR, 13C NMR, 1H-IH COSY, HMBC, HMQC, UV-Vis absorption and emission, CV and TGA experiments to study PQ and benzil that provided the following novel results. （1） The 1H NMR（CDC13） of PQ show δ 8.19（H1）, 8.02（H4）, 7.72（H3）, 7.47（H2） instead of an earlier reported 8.25（H4）, 8.08（H1）, 7.80（H2）, 7.55（H3）; （2） in the 13C NMR（CDCl3）, the C9/C10（C=O） signal of PQ appears upfield（6 180.3） compared to C9/Cl0（C=O） signal of benzil（6 194.5）, which shows higher electrophilic character（more attractive for nucleophiles） of C9/C10（C=O） of benzil; （3） the first 2max for the UV-Vis absorption and emission of PQ are blue-shifted compared to benzil despite increased conjugation attributed to the different symmetries（C2v for PQ and C2h for Benzil） of the two molecules; （4） the emission spectrum of benzil is broader compared to that of PQ due to slower relaxation of the excited state; （5） The CV study shows that PQ and benzil are good electron acceptors and PQ shows a better reduction process than benzil due to an extra ring that provides stability for the reduced species（mono or diradical anions）; （6） TGA shows the higher thermal stability of PQ than benzil attributed to the presence of phenanthrene unit in PQ.

Research on the Relationship between Molecular Activity of Additives and Lubricating Performance of Aluminum Rolling Oil

In this paper,an ab initio,local density functional(LDF)method was used to explore the relationship between the molecular properties of additives and the lubricating performance of aluminum rolling oil.The structural properties of butyl stearate,dodecanol,docosanol,and methyl dodecanoate were studied according to the density functional theory.The calculated data showed that the atoms in or around the functional groups might be likely the reacting sites.Because of the different functional groups and structure of ester and alcohol,two types of complex additives,dodecanol and butyl stearate,methyl dodecanoate and butyl stearate,respectively,were chosen for studying their tribological properties and performing aluminum cold rolling experiments.The test results agreed with the calculated results very well.The complex ester,viz.methyl dodecanoate and butyl stearate,had the best lubricating performance with a friction coefficient of 0.084 1 and a permissive-rolling thickness of 0.040 mm as compared with that of dodecanol-butyl stearate-base oil formulation.

Morphological and molecular identification of Neopestalotiopsis clavispora causing flower blight on Anthurium andraeanum in Thailand

Flower blight on anthurium(Anthurium andraeanum)was observed during August 2018 on an anthurium cultivation farm in the Songkhla Province of southern Thailand.The fungal isolate was identified as Neopestalotiopsis clavispora based on the morphology and DNA sequence of the internal transcribed spacer(ITS),translation elongation factor 1-α(tef1-α),andβ-tubulin(tub)genes.The phylogenetic tree,based on the combined sequences of ITS,tef1-α,and tub,confirmed this pathogen as N.clavispora.Pathogenicity of the species was confirmed according to Koch’s postulate:N.clavispora could infect anthurium.To the best of our knowledge,this is the first report of N.clavispora as a pathogen of anthurium.

THE DYNAMIC PROPERTIES FOR THE PROTEIN MOLECULAR SYSTEM

In this paper, a new theory for the dynamic properties of protein molecular system have been proposed by means of the analysis of the characteristics of the collective excitations generated under the localized fluctuation and the deformation of structure of the protein. Some new results obtained from this study show that the Davydov theory is an approximate and disadvantegeous theory.

ELECTRONEGATIVITY TOPOLOGICAL INDEX AND ITS APPLICATION IN CORRELATION WITH MX,MX_2,MX_3,MX_4 MOLECULAR PROPERTIES

A New electronegativity topological index is defined and used to correlate with properties of MX,MX_2,MX_3,MX_4.

Effect of Chirality on the Electronic Transport Properties of the Thioxanthene-Based Molecular Switch

Based on the nonequilibrium Green function method and density functional theory calculations, we theoretically investigate the effect of chirality on the electronic transport properties of thioxanthene-based molecular switch. The molecule comprises the switch which can exhibit different chiralities, that is, cis-form and trans-form by ultraviolet or visible irradiation. The results clearly reveal that the switching behaviors can be realized when the molecule converts between cis-form and trans-form. ~urthermore, the on-off ratio can be modulated by the chirality of the carbon nanotube electrodes. The maximum on-off ratio can reach 109 at 0.4 V for the armchair junction, suggesting potential applications of this type of junctions in future design of functional molecular devices.

A Modifi ed Molecular Structure Mechanics Method for Analysis of Graphene

Based on molecular mechanics and the deformation characteristics of the atomic lattice structure of graphene, a modifi ed molecular structure mechanics method was developed to improve the original one, that is, the semi-rigid connections were used to model the bond angle variations between the C-Cbonds in graphene. The simulated results show that the equivalent space frame model with semi-rigid connections for graphene proposed in this article is a simple, efficient, and accurate model to evaluate the equivalent elastic properties of graphene. Though the present computational model of the semi-rigid connected space frame is only applied to characterize the mechanical behaviors of the space lattices of graphene, it has more potential applications in the static and dynamic analyses of graphene and other nanomaterials.

Electron Transport Properties of Two-Dimensional Si_1P_1 Molecular Junctions

We focus on two new 21） materials, i.e., monolayer and bilayer silicon phosphides （Sil P1）. Based on the elastic- scattering Green＇s function, the electronic-transport properties of two-dimensional monolayer and bilayer Au- Si1P1-Au molecular junctions are studied. It is found that their bandgaps are narrow （0.16eV for a monolayer molecular junction and 0.26 e V for a bilayer molecular junction）. Moreover, the calculated current-voltage char- acteristics indicate that the monolayer molecular junction provides constant output current （20 hA） over a wide voltage range, and the bilayer molecular junction provides higher current （42 hA）.

Electron Transport Properties of Two-Dimensional Monolayer Films from Au-P-Au to Au-Si-Au Molecular Junctions

We investigate the electronic-transport properties of two-dimensional monolayer films from Au-P-Au molecular junction to Au-Si-Au molecular junction using elastic scattering Green＇s function theory. In the process of replacing the P atoms with Si atoms every other line from the middle of monolayer blue phosphorus molecular structure, the substitution of Si atoms changes the properties of Au-P-Au molecular junction significantly. Interestingly, the current value has a symmetric change as a parabolic curve with the peak appearing in Au-Si_1P_1-Au molecular junction, which provides the most stable current of 15.00 nA in a wide voltage range of 0.70-2.70 V.Moreover, the current-voltage characteristics of the structures indicate that the steps tend to disappear revealing the property similar to metal when the Si atoms dominate the molecular junction.

All-electron ZORA triple zeta basis sets for the elements Cs-La and Hf-Rn

Segmented all-electron basis set of triple zeta valence quality plus polarization functions(TZP)for the elements of the fifth row to be used together with the zero-order regular approximation(ZORA)is carefully constructed.To correctly describe electrons distant from atomic nuclei,the basis set is augmented with diffuse functions giving rise to a set designated as ATZP-ZORA.At the ZORA-B3LYP theoretical level,these sets are used to calculate the ionization energy and mean dipole polarizability of some atoms,bond length,dissociation energy,and harmonic vibrational frequency of diatomic molecules.Then,these results are compared with the theoretical and experimental data found in the literature.Even considering that our sets are relatively compact,they are sufficiently accurate and reliable to perform property calculations involving simultaneously electrons from the inner shell and outer shell.The performances of the ZORA and second-order Douglas-Kroll-Hess Hamiltonians are evaluated and the results are also discussed.

Machine Learning-Assisted High-Throughput Virtual Screening for On-Demand Customization of Advanced Energetic Materials

Finding energetic materials with tailored properties is always a significant challenge due to low research efficiency in trial and error.Herein,a methodology combining domain knowledge,a machine learning algorithm,and experiments is presented for accelerating the discovery of novel energetic materials.A high-throughput virtual screening(HTVS)system integrating on-demand molecular generation and machine learning models covering the prediction of molecular properties and crystal packing mode scoring is established.With the proposed HTVS system,candidate molecules with promising properties and a desirable crystal packing mode are rapidly targeted from the generated molecular space containing 25112 molecules.Furthermore,a study of the crystal structure and properties shows that the good comprehensive performances of the target molecule are in agreement with the predicted results,thus verifying the effectiveness of the proposed methodology.This work demonstrates a new research paradigm for discovering novel energetic materials and can be extended to other organic materials without manifest obstacles.

A Novel Isoenzyme of CuZn-superoxide Dismutase from Nicotiana tobacum

An isoenzyme of CuZnsuperoxide dismutase, denoted as CuZnSODⅢ, has been separated and purified from Nicotiana Tobacum (tobacco) leaves to apparent homogeneity. Its molecular mass is 22976.6Da. It is composed of one subunit, which is consisted of 187 amine acid residues and contains 1 copper and 0.5 zinc atom. The activation energy of the thermal denaturation process has been obtained as about 143.5kJmol-1. Meanwhile, some properties of spectra were investigated.

Structural, Pasting, and Thermal Properties of Ultra-high Pressure-treated Lotus Seed Starch

Lotus seed starch （15%, w/w） was subjected to ultra-high pressure （UHP） at 500 MPa for 10～60 min. The effects of UHP on the structural, pasting, and thermal properties of starch were investigated using solid-state 13C CP/MAS NMR, differential scanning calorimetry （DSC）, HPSEC-MALLS-RI, and a rapid visco analyzer. The 13C CP/MAS NMR results revealed a reduction in the relative crystallinity and peak intensity of the crystalline state with increasing the UHP time. The molecular weight of native starch was 1.433 × 107 Da, which was higher than that of the UHP-treated starch. Viscograms of UHP-treated starch revealed an increase in paste viscosity, peak time, and pasting temperature and a reduction in breakdown and setback viscosity compared to the native starch. Furthermore, the DSC results showed a reduction in gelatinization temperature and gelatinization enthalpy with increasing the UHP time.

Characterization of A-and B-type starch granules in Chinese wheat cultivars

Starch is the major component of wheat flour and serves as a multifunctional ingredient in food industry. The objective of the present study was to investigate starch granule size distribution of Chinese wheat cultivars, and to compare structure and functionality of starches in four leading cultivars Zhongmai 175, CA12092, Lunxuan 987, and Zhongyou 206. A wide variation in volume percentages of A- and B-type starch granules among genotypes was observed. Volume percentages of A- and B-type granules had ranges of 68.4–88.9% and 9.7–27.9% in the first cropping seasons, 74.1–90.1% and 7.2–25.3% in the second. Wheat cultivars with higher volume percentages of A- and B-type granules could serve as parents in breeding program for selecting high and low amylose wheat cultivars, respectively. In comparison with the B-type starch granules, the A-type granules starch showed difference in three aspects：（1） higher amount of ordered short-range structure and a lower relative crystallinity,（2） higher gelatinization onset（To） temperatures and enthalpies（ΔH）, and lower gelatinization conclusion temperatures（Tc）,（3） greater peak, though, and final viscosity, and lower breakdown viscosity and pasting temperature. It provides important information for breeders to develop potentially useful cultivars with particular functional properties of their starches suited to specific applications.

QSPR Analysis of the Physicochemical Properties for Phthalic Acid Esters

Based on quantitative structure-property relationship （QSPR） of organic compounds, the molecular connectivity indices of 21 phthalic acid ester compounds were extracted. Relationship between the physicochemical properties （n-octanol/air partition coefficient, vapor pressure, water solubility） and the molecular connectivity indices of phthalic acid ester compounds have been established by multiple linear regression （MLR） method. The results showed that the zero-order valence connectivity index （0Xu） is the topology parameter which affects octanol/water partition coefficient and water solubility, and the topology parameter which affects vapor pressure is the first-order connectivity index （1X）. This indicated to a certain extent_that the molecular connectivity indices can be well used to express the quantitative relationship between the physicochemical properties and structure descriptions of phthalic acid ester compounds. The models constructed have good robustness and highly predictive capability.

Thermal properties of polyurethane elastomer with different flexible molecular chain based on para-phenylene diisocyanate

This work focuses on the relationship between flexibility of molecular chains and thermal properties of polyurethane elastomer（PUE）, which laid the foundation of further research about how to improve thermal properties of PUE. A series of PUE samples with different flexibility of molecular chains was prepared by using 1,4-butanediol（1,4-BDO）/bisphenol-a（BPA） blends with different mole ratios including9/1, 8/2, 7/3, 6/4 and 5/5. As comparison, PUE extended with pure 1,4-BDO and BPA was also synthesized.These samples were characterized by differential scanning calorimetry（DSC）, thermogravimetric analysis（TGA）, dynamic mechanical analysis（DMA）, etc. The results showed that with the decrease in flexibility of molecular chains the glass transition temperature（Tg） increased and low-temperature properties became worse. Besides, all samples had a certain degree of microphase separation, and soft segments in some samples were crystallized, i.e. the decreasing flexibility of molecular chains led to the impossibility of chains tightly packing and crystalline domains forming so that the degree of microphase separation decreased and the thermal properties became worse.