Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Structures of N—（2,3,4,6—Tetra—O—acetyl—β—D—glycosyl） thiocarbamic Benzoyl Hydrazine

The crystal structure of N-(2,3,4,6-tetra-O-acetyl-β-D-gly-cosyl)-thiocarbamic benzoyl hydrazine(C22H27N3O9S) was determined by X-ray diffracton method.The hexopyranosyl ring adopts a chair conformation.All the ring substituents are in the equatorial positions.The acetoxyl-methyl group is in synclinal conformation.The S atom is in synperiplanar conformation while the benzoyl hydrazine moiety is anti-periplanar.The thiocarbamic moiety is almost companar with the benzoyl hydrazine group.There are two intramolecular hydrogen bonds and one intermolecular hydrogen bond for each molecule in the crystal structure.The molecules form a network structure through intermolecular hydrogen bonds.     

Molecular dynamics simulations of the hydration of poly(vinyl methyl ether):Hydrogen bonds and quasi-hydrogen bonds

Atomistic detailed hydration structures of poly(vinyl methyl ether)(PVME) have been investigated by molecular dynamics simulations under 300 K at various concentrations. Both radial distribution functions and the distance distributions between donors and acceptors in hydrogen bonds show that the hydrogen bonds between the polymer and water are shorter by 0.005 nm than those between water molecules. The Quasi-hydrogen bonds take only 7.2% of the van der Waals interaction pairs. It was found the hydrogen bonds are not evenly distributed along the polymer chain,and there still exists a significant amount(10%) of ether oxygen atoms that are not hydrogen bonded to water at a concentration as low as 3.3%. This shows that in polymer solutions close contacts occur not only between polymer chains but also between chain segments within the polymer,which leads to inefficient contacts between ether oxygen atoms and water molecules. Variation of the quasi-hydrogen bonds with the concentration is similar to that of hydrogen bonds,but the ratio of the repeat units forming quasi-hydrogen bonds to those forming hydrogen bonds approaches 0.2. A transition was found in the demixing enthalpy at around 30% measured by dynamic testing differential scanning calorimetry(DTDSC) for aqueous solutions of a mono-dispersed low molecular weight PVME,which can be related to the transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27%. The transition of the fractions of hydrogen bonds and quasi-hydrogen bonds at ～27% can be used to explain the demixing enthalpy transition at 30% at a molecular scale. In addition,at the concentration of 86%,each ether oxygen atom bonded with water is assigned 1.56 water molecules on average,and 'free' water molecules emerge at the concentration of around 54%.     

MONTE CARLO SIMULATION ON AQUEOUS SOLUTION OF BIOLOGICAL MOLECULES——ALANINE SOLUTION

The Monte Carlo simulation is performed for a cluster consisting of a neutral alanine molecule surrounded by 56 water molecules. The average water-water and alanine-water interaction energies are found. The space surrounding the alanine molecule is divided into three regions, where the central atoms are C' atom for the earboxyl group region, N atom for the amino group region and C~β atom for the methyl group region. The water-water and water-alanine interaction energies as functions of the distance between the oxygen atom in a water molecule and the central atom in each region are calculated. In each region the orientational correlation function for the dipole moments of water molecules, the radial distribution function for the oxygen and hydrogen atoms of water molecules are evaluated. In addition, the numbers of water molecules in the first solvation shells of each region and of entire alanine molecule are also counted.     

X-RAY STUDIES ON THE STRUCTURE OF DES-PENTAPEPTIDE INSULIN AT 2.4 RESOLUTION——THE DPI MOLECULE AND ITS STRUCTURAL RELATIONSHIP WITH INSULIN

The structure of the monomeric insulin analogue des(B26—B30) insulin is presented.; A detailed comparison with the 2Zn insulin structures shows that while there are some large changes in the structure, the basic secondary structural units maintain their integrity. The DPI structure is broadly similar to molecule Ⅰ in the 2Zn structure, and in this respect is like other crystal forms of insulin. In addition to changes on the surface of the structure there are some subtle but extensive changes in the heart of the molecule. The molecules are closely packed in the crystal with many and varied contacts, including a complex network of protein-cadmium interactions and a considerable number of water mediated contacts. The molecular surface has an unusually large number of hydrophobic groups which tend to cluster in a thick band running around the protein. The crystal structure is well ordered, indeed the clarity of some side chains and the definition of the water molecules is superior to that found in the mor     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Rapid Evaluation of Individual Hydrogen Bonding Energies in Linear Water Chains

A model is proposed to rapidly evaluate the individual hydrogen bonding energies in linear water chains. We regarded the two O--H bonds of a water molecule as two dipoles. The magnitude of the O--H bond dipole mo- ment can be varied due to the other water molecules＇ presence. An analytic potential energy function, which explicitly contains the permanent dipole-dipole interactions, the polarization interactions, the van der Waals interactions and the covalent interactions, was therefore established. The individual hydrogen bonding energies in a series of linear water chains were evaluated via the analytic potential energy function and compared with those obtained from the CP-corrected MP2/aug-cc-pVTZ calculations. The results show that the analytic potential energy function not only can produce the individual hydrogen bonding energies as accurately as the CP-corrected MP2/aug-cc-pVTZ method, but is very efficient as well, demonstrating the model proposed is reasonable and useful. Based on the individual hy- drogen bonding energies obtained, the hydrogen bonding cooperativity in the linear water chains was explored and the natures of the hydrogen bonding in these water chains were discussed.     

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.     

Orbital deletion procedure and its applications

The orbital deletion procedure is introduced, which is suited to quantitatively investigating the electronic delocalization effiect in earboeations and boranes. While the routine, ab initio molecular orbital methods can generate wavefunetions for real systems where all electrons are delocalized, the present orbital deletion procedure can generate wavefunctions for hypothetical reference molecules where electronic delocalization effect is deactivated. The latter wavefunetion normlly corresponds In the most stable resonance structure in terms of the resonance theory. By comparing and analyzing the delocalized and the localized wavefunetions, one can obtain a quantitative and instinct pieture to show how electronic deloealizalion inside a molecule affects the molecular structure, energy as well as other physical properties. Two examples are detailedly discussed. The first is related to the hypercoujugation of alkyl groups in carbocations and a comparison of the order of stability of carbocations is made, T     

Periodic tables of diatomic and triatomic molecules

The Mendeleev periodic table of atoms is one of the most important principles in natural science. However, there is shortage of analog for molecules. Here we propose two periodic tables, one for diatomic molecules and one for triatomic molecules. The form of the molecular periodic tables is analogous to that of Mendeleev periodic table of atoms. In the table, molecules are classified and arranged by their group number G, which is the number of valence electrons, and the periodic number P, which represents the size of the molecules. The basic molecular properties, including bond length, binding energy, force constant, ionization potential, spin multiplicity, chemical reactivity, and bond angle, change periodically within the tables. The periodicities of diatomic and triatomic molecules are thus revealed. We also demonstrate that the periodicity originates from the shell-like electronic configurations of the molecules. The periodic tables not only contain free molecules, but also the "virtual" molecules present in polyatomic molecules. The periodic tables can be used to classify molecules, to predict unknown molecular properties, to understand the role of virtual molecules in polyatomic molecules, and to initiate new research fields, such as the periodicities of aromatic species, clusters, or nanoparticles. The tables should be of interest not only to scientists in a variety of disciplines, but also to undergraduates studying natural sciences.     

Isolation,Crystal Structure and Na~+/K~+-ATPase Inhibitory Activity of 1β-Hydroxydigitoxigenin

The title compound 1β-hydroxydigitoxigenin(1) was isolated from the ethanol extract of the roots of Streptocaulon juventas. The crystal structure of 1, C_(23)H_(34)O_5·H_2O, was determined by Synchrotron X-ray diffraction analysis due to small crystal size(0.14 mm × 0.04 mm × 0.01 mm). The crystal belongs to monoclinic, space group P21, with a = 7.6624(15), b= 13.460(3), c = 10.370(2) ?, b = 92.40(3)°, V = 1068.6(4) ?3, Z = 2, Mr = 406.50, Dx = 1.263 g/cm3, λ(synchrotron) = 1.2399 ?, μ(synchrotron 1.23990) = 0.333 cm~(-1), F(000) = 550, S = 1.059, R = 0.0625 and w R = 0.1687 for 4247 unique reflections, of which 3687 were observed(I 2σ(I)). The asymmetric unit contains one independent molecule of 1 and one water molecule which are connected through hydrogen bonds. The conformation of 1 in crystalline state is in good agreement with the solution structure in methanol as indicated by ~1H-NMR analysis. The absolute configuration of 1 could be assigned by referring to the known configuration of the lactone ring at C(17b). In the solid state, intermolecular hydrogen bonds involving carbonyl group in the lactone moiety and the hydroxyl groups in the steroid moiety ester linked adjacent molecules into a three-dimensional network. Compound 1 showed significant inhibition on Na+/K+-ATPase with an IC50 of 2.46 mM, which is stronger thiocarbonylbufalin but weaker than a close analog digitoxigenin, suggesting that a lactone ring is important and the substitution of a hydroxyl group at C(1) is not favored for the inhibition of Na~+/K~+-ATPase.     

Formation Sites and Microscopic Conformation Study on the Konjac Glucomannan Molecular Helices

<正>In this work,the formation sites,helical parameters and hydrogen bond positions of Konjac glucomannan molecular helices were investigated using molecular dynamic simulation method.To our interest,the KGM chain is mainly composed by local left and right helix structures. The formation sites of KGM chain might locate at the chain-segments containing acetyl groups,and the left helix is the favorable conformation of KGM.Temperature-dependent molecule conformation study indicates that the right helix is dominant when the temperature is lower than 343 K,above which,however,the left helix is dominating(right helix disappears).In addition,intramolecular hydrogen bonds in the left helix can be found at the-OH groups on C(2),C(4)and C(6)of mannose residues;comparably,the intramolecular hydrogen bonds in the right helix can be mainly observed at the-OH groups on C(4)and C(6)of the mannose residues and C(3)of the glucose residues.In conclusion,molecular dynamic simulation is an efficient method for the microscopic conformation study of glucomannan molecular helices.     

Synthesis,Characterization and Antibacterial Activities Study of a Pharmaceutical Cocrystal of Artesunate and 4,4’-Bipyridine

We report here a cocrystal with artesunate as the active pharmaceutical ingredient(API) and a pharmaceutical intermediate 4,4?-bipyridine as the cocrystal former(CCF). The analysis of single-crystal X-ray diffraction demonstrates that the eutectic structural unit consists of two artesunate molecules and one 4,4?-bipyridine molecule with their ratio to be 2:1. The carboxyl group on artesunate acts as a donor, and the acceptor is N on 4,4?-bipyridine, forming an O–H···N hydrogen bond. The appearance of new diffraction peaks in the X-ray powder diffraction pattern also indicates the formation of new phases. The PXRD results indicated a pure phase for the synthesized sample. The cocrystal is slightly soluble in water. Antimicrobial activities showed that the cocrystal displayed effective inhibition of different bacteria.     

Synthesis and Crystal Structure of a Complex of Melamine with Benzoic Acid

A new complex of melamine（MA） with benzoic acid（HBA） was prepared, affording [（HMA＋）（BA-）]-2H2O. Each HBA molecule is deprotonated and one triazine nitrogen atom of MA is protonated. The adjacent HMA＋ cations are related via an inverse center to form ribbons with a pair of N--H…N hydrogen bonds. COO- groups of BA- anions are hydrogen bonded to alternate sides of the （HMA＋）∞ ribbons to generate indention ID tapes, which are extended into a 3D structure via N--H…O- and N--H…OW hydrogen bonds and π-π stacking interactions. Predominant patterns of the hydrogen bond present in the complex are anion/water and amino/water tape structures. The hydrogen-bonding patterns consist of alternate 6, 10-membered rings sharing two edges. Infrared（IR） spectroscopy conforms that proton transfer has taken place in the complex.     

THEORETICAL STUDIES ON THE SUBSTITUTION EFFECT OF FLUORINE ON ETHANE

<正> The substitution effect of fluorine on ethane has been investigated by means of studying the properties of the charge distribution at the bond critical points with the theory of atoms in molecule.It is found that the major substitution effects of fluorine atom are positive a inductive and polarity effect.At the same time,fluorine atom partially provides π electrons to other chemical bonds by means of hy-perconjugation in molecules with two fluorine atoms and one or two carbon atoms in the same plane,and these effects are reflected in the quantity of bond ellipticity,Laplacian and the charge density of charge distribution at the bond critical points.The substitution of hydrogen by fluorine in ethane strengthens all the bonds in substituted ethanes.Other effects originating from the substitution of hydrogen by fluorine have also been discussed.     

Transfer Hydrogenation of C= C Double Bonds Catalyzed by Ruthenium Amido-Complexes: Scopes, Limitation and Enantioselectivity

The reduction of C = C double bonds is one of the most fundamental synthetic transformations and plays a key role in the manufacturing of a wide variety of bulk and fine chemicals. Hydrogenation of olefinic substrates can be achieved readily with molecular hydrogen in many cases, but transfer hydrogenation methods using suitable donor molecules such as formic acid or alcohols are receiving increasing attention as possible synthetic alternatives because it requires no special equipment and avoids the handling of potentially hazardous gaseous hydrogen.     

Syntheses and Crystal Structures of Two 3D Zinc(II) Compounds Involving Coordination and Hydrogen Bonds

1 INTRODUCTION Self-assembly through coordination and hydrogen bonds has been proved to be a powerful tool for con- structing functional organic crystalline materials[1~4]. Except for the important role of H-bonds in the sta- bilization of structures, hydrogen bonding groups namely hydroxyl, amide groups in adjacent coor- dination polymeric chains or discrete lamellas can form hydrogen bonds, which allow for the assembly of well-formed crystalline solid[5, 6]. Our recent inte- rest is foc…     

STUDIES ON THE CRYSTAL STRUCTURE OF (D-Ala)-B0 PORCINE INSULIN AT 1.9 RESOLUTION

The crystal structure of (D-Ala)-B0 porcine insulin has been determined, using data to 1.9 and atomic parameters of 2 Zn porcine insulin as a starting model, and through the use of the difference method and the restrained least square method, to a final R-factor of 0.211 and r. m. s. deviation of 0.057 for the bond lengths. The electron densities of B0 residues were very clear. Introduction of B0 residues into the molecules had reduced the thermal vibration of the N-terminus of B-chain for both molecules Ⅰ and Ⅱ and made the molecules pack closer in the crystal The obvious differences between the crystal structures of 2 Zn and (D-Ala)-B0 porciue insulin were the conformations of partial polar groups around the possible receptor binding surface and the assembly mode of two helixes of A-chain in molecule I. In the local environment of the N-terminus of Bchain there were great differences between the crystal structures of(D-Ala)-B0 porcine insulin, (Trp)-B1 porcine insulin and Des B1(Phe) bovine insulin.     

Synthesis of Substituted 3H-Indole-modified b-Cyclodextrin

The hydrophobic cavities of cyclodextrins and the inclusion with various organic molecules in the aqueous solution make them useful in chemical and biological activities1, one of which is the modified cyclodextrins acting as indicators of molecular recognition. Cyclodextrins, which are spectroscopically inert, can be converted into spectroscopically active compounds by modifing one or two of the hydroxy groups with appropriate chromophores, and used as molecular sensor due to the capability of…     

THE POSSIBLE MECHANISM OF BINDING INTERACTION OF INSULIN MOLECULE WITH ITS RECEPTOR

Detailed structural comparisons and investigation of DPI, 2Zn insulin and some other derivatives of insulin were performed by the least-squares superimposition technique and the graphics technique. It is pointed out in this paper that the binding interaction with the receptor molecule should take place mainly on an amphipathic surface of the insulin molecule. In the middle, there is a hydrophobic surface with an area of about 150 consisting of many hydrophobic residues; while the polar or charged groups distributing around the hydro. phobic surface construct a hydrophilic zone. The hydrophobic surface is usually covered by the extended B-chain C-terminal peptides with great mobility and protected from the solvent molecules. The angle between the amphipathic surface and the surface of dimerization is about 20 degrees. The results from the detailed structural comparison between A1-(L-Trp) insulin and A1-(D-Trp) insulin have provided a very good explanation to their great difference in biological activity,