Molecular configuration of α-furil

X-ray diffraction studies on α-furil single crystals reveal that the two parts of the molecule are connected with a twofold symmetry axis perpendicular to the C-C single bond connecting the two carbonyl groups. The dihedral angles between the two halves of the molecule and the carbonyl/furan moieties are 46.7° and 2.7°, respectively.     

Molecular modeling of rice Rubisco

Molecular model of rice Rubisco has been constructed by molecular modeling method on a computer graphics workstation using graphics software TOM-FRODO and QUANTA/CHARMm,based on the three-dimensional structure of spinach Rubisco.The molecular modeling was carried out in the following procedure:amino-acid sequence substitution;manual adjustment of the initial model;and energy minimization.The three-dimensional structure of the quaternary complex Rubisco-CO2·Mg2+·CABP of rice Rubisco has also been modeled and optimized using the program package XPLOR.The main-chain structure of rice Rubisco does not show obvious difference from that of spinach Rubisco,and the side-chains are located in the most favorable positions and orientations.The active-site structures are basically the same for the two species.The mutant Leu335→Arg of rice Rubisco has been designed using the graphics software TURBO-FRODO and the program package XPLOR.Energy computation suggests that this mutation might increase the carboxylation     

Molecular Simulations using Spherical Harmonics

Computer-aided drug design is to develop a chemical that binds to a target macromolecule known to play a key role in a disease state. In recognition of ligands by their protein receptors, molecular surfaces are often used because they represent the in-teracting part of molecules and they should reflex the comple-mentarity between ligand and receptor. However, assessing the surface complementarity by searching all relative position of two surfaces is often computationally expensive. The comple-mentarity of lobe-hole is very important in protein-ligand inter-actions. Spherical harmonic models based on expansions of spherical harmonic functions were used as a f‘mgerprint to ap-proximate the binding cavity and the ligand, respectively. This defines a new way to identify the complementarity between lobes and holes. The advantage of this method is that two spherical harmonic surfaces to be compared can be defined sep-arately. This method can be used as a filter to eliminate candi-dates among a large number of conformations, and it will speed up the docking procedure. Therefore, it is possible to select complementary ligands or complementary conformations of a ligand and the macromolecules, by comparing their fingerprints previously stored in a database.     

Molecular configuration of α-naphthil

X-ray crystallographic studies on the molecular structure of α-naphthil reveal that the intercarbonyl dihedral angle is 87.29° whereas the naphthalene groups make angles of 4.26° and 6.98° with the respective carbonyl planes. The two naphthalene moieties are twisted about their central bonds.     

Molecular structure of diatomic lanthanide compounds

The molecular constants of selected diatomic lanthanide compounds (LaH, LaO, LaF, EuH, EuO, EuF, EuS, GdO, GdF, GdH, YbH, YbO, YbF, YbS, LuH, LuO and LuF) have been calculated by using relativistic small-core pseudopotentials and optimized (14s13p10d8f6g)/ [6s6p5d4f3g] valence basis sets. The results are in good agreement with available experimental data, with exception of YbO and LuF. The reasons for the discrepancies in case of YbO are due to a complicated mixing of configurations in the ground state, whereas in case of LuF the binding energy estimated by experimentalists appears to be too low.     

Molecular Mechanics Study on Asymmetry Catalysis

Theasymmetrycatalysisisanimportantchemicalreactionwidelyusedinbiology,pharmacyalldagriculture.Itispreferredtoenantioselectivehydrogenationofmethylpyruvate(MP)oversuppoFtedplatiniumnanoclusters.Cinchonidine(CD)isamodifier,aco-catalysttothereaction.Withoutthemodifier,therewouldbenoenantioselectivitytothehydrogenationofpyruvate.Inordertoobtainbetterunderstandingofthemechanismofthereaction,especiallytheroleofthemoditler,thepresentstudybymolecularmodelinghasbeenperformedandtheresultsarereportedhe…     

Crystal and Molecular Structure of OMPCTF

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Crystal and Molecular Structure of Quinide

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Progress in Molecular Dynamics and Hansen Solubility Parameters of Low Molecular Weight Gels北大核心CSCD

Recently,the use of computational methods such as Molecular Dynamics（MD）simulations and Hansen Solubility Parameters （HSPs）to study the behavior of small molecule gelators has attracted much attention. MD simulation is a computational method based on classical mechanics and is one of the preferred techniques for understanding the process of small molecule gelators. The MD simulation can more accurately analyze the gelation trend or assembly behavior of small molecule gelators,dynamically and graphically display the self-assembly process,effectively reveal the relationship between the structure of small molecule gelators and related gelation behavior,and quantitatively analyze non-covalent bond interactions such as hydrogen bonds,π-π stacking,van der Waals interactions,ionic bonding and solvophobic interactions. By performing molecular dynamics simulations on known gelators/non-gelators,parameters related to gelation behavior in the simulated data are extracted,and the linear correlation is measured by fitting the Pearson correlation coefficient to finally predict the gelation behavior of a certain class of small molecules. On the other hand,the empirical model developed according to the HSPs is the most representative,which consists of the energy of dispersion interaction（δd）,the energy of polar interaction（δp）and H-bonding energy（δh ）between molecules. These three parts determine the coordinate point of the three-dimensional space（Hansen space）. According to the range of the point,it can be determined whether the organic small molecule can form a gel in a specific solvent. In this paper,representative works published recently in the field of organic small molecule gels by using MD simulations and empirical models are reviewed. Some comments on the assembly behavior of gelators,the regulation and prediction of non-covalent bond interactions on gelation ability are made. © 2022, Science Press (China). All rights reserved.     

Journal of Molecular Catalysis(China)

The Journal of Molecular Catalysis(China)was first publishedin 1987 by the approval of the State Science and Technology Com-mission.It is an academic periodical circulated both domestically andinternationally.     

Dynamics Studies on Molecular Diffusion in Zeolites

1 INTRODUCTION Zeolites have attracted much attention in both scientific and industrial areas for their special characteristics and multiple uses. Zeolites are composed of TO4 (T = Si, Al, Ga, P, etc.) tetrahedra which are connected with each other by sharing oxygen atoms to produce a complex and repetitive three-dimensional atom network with regular molecular dimension cavities joined by channels. Shape selectivity is the most important property of zeolites. Combined with the possib…     

The Crystal and Molecular Structure of Fargesin

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Crystal and Molecular Structure of Cyanuric Acid

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Molecular electronics—the future of bioelectronics

In the last decade, molecular electronics, as an active frontier of interdisciplinary research areas, has become one of the most rapidly developing fields, and attracted worldwide interests. The fundamental element of molecular electronics is a molecular device or a supramolecular device, which is an organized molecular system constructed mainly by organic molecules or biomolecules that have some specific functions in signal detection, process, storage, and transmission through chemical or physical interactions at molecular or supramolecular levels. A molecular device (MD) can involve chemical information processes, and be relatively easy to realize a large number of links between the molecules. The links can be controlled by the external signals. These are the expected features of molecular computing and directly involve chemical and biological processes. MD may overcome some limitations of the solid-state chips, and can be directly applied to chemical and biological processes. Molecular electronics is a part of bioelectronics. It will play an important and revolutionary role in the next century. This paper intends to review the research activities of molecular electronics in China, particularly in LMBE.     

Molecular and electronic structure of δ-valerothiolactone

The crystal structure of the six-member heterocyclic δ-valerothiolactone (1-thiocycloalkan-2-one) compound has been determined by X-ray diffraction at low temperature, revealing that its skeleton adopts a half-chair conformation. The conformation around the thioester group is almost planar with an anti orientation of the C=O double bond with respect the S-C single bond [C(2)-S(1)-C(6)-O(1) = 176.26(8)°]. The skeletal parameters, especially valence angles [∠C5-C6-S = 121.19(6)°, ∠O=C6-C5 = 122.25(8)°, ∠C6-S-C2 = 106.80(4)°], differ from those typically found in acyclic thioester compounds, symptomatic of the presence of strain effects. The conventional ring strain energy was determined to be 7.5 kcal/mol at the MP2/6-311++G(d,p) level of calculation within the hyperhomodesmotic model approximation. Moreover, the valence electronic structure was investigated by HeI photoelectron spectroscopy assisted by quantum chemical calculations at the OVGF/6-311++G(d,p) level of theory. The first three bands at 9.35, 9.50, and 11.53 eV denote ionizations related with the n(S), n(O), and π(C=O) orbitals, respectively, demonstrating the importance of the -SC(O)- group in the outermost electronic properties.     

A Novel Pyrazoline-based Starburst Amorphous Molecular Material

A pyrazoline-containing starburst molecule, 4,4‘,4““-tris[(1,3-diphenyl-4,5-dihydro-1H-pyrazol)-5-yl]-triphenylamine (Tris-5-DPP), was synthesized in a facile way, which can form amorphous thin films with glass transition temperature as high as 136℃.     

Reconstitution of Motor Proteins through Molecular Assembly

What is the most favorite and original chemistry developed in your research group?The most favorite and original chemistry developed in my research group is about the reconstitution of motor proteins in artificially designed and assembled units.It is based on the molecular assembly technique,but the method is different from the conventional approach.