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.     

CRYSTAL AND MOLECULAR STRUCTURE OF DEHYDROCRYDALINE CHLORIDE

The crystals of alkaloid Dehydrocrydaline chloride (C_(22)H_(24)NO_4·HCl) belong to the orthorhombic system. The space group is D_(2k)~(14)-Pbcn with the unit cell parameters of a=8.528,b=23.317 and c=24.798, and eight molecules per unit cell. The coordinates for all the non-hydrogen atoms were found by using direct methods and Fourier syntheses. During the course of refinement of this structure (using least squares and difference Fouriers), it was discovered that there are 4.5 water molecules with different occupancies in one asymmetric volume of the unit cell. The anisotropic refinement of non-hydrogen atoms and the isotropic refinement of non-aqueous hydrogen atoms led to a final R-factor of 0.053. Water molecules formed a relatively complex network around chloride ion.In this paper the small molecule structure and the network of water molecules are described.     

Theoretical Study of Interaction between Apalutamide Anticancer Drug and Thymine by DFT Method

The main purpose of this study is a better comprehension of the non-bonded interaction between an anticancer drug apalutamide and deoxyribonucleic acid(DNA). In the present work, the interaction between anticancer drug apalutamide and one of the DNA bases called 2'-deoxythymidine 5'-monophosphate(thymine) by Density Functional Theory(DFT) calculations in the solvent water has been investigated for the first time. The non-bonded interaction effects of the molecule apalutamide with thymine on the electronic properties, chemical shift tensors and natural charges have been also detected. The natural bond orbital(NBO) analysis was performed for determining the role of electron donor and acceptor of the molecules apalutamide and thymine at the complex thymine/apalutamide. Both Electron location function(ELF), localized orbital locator(LOL) and quantum theory of atoms in molecules(QTAIM) analysis were carried out in order to determine the chemical bond nature in the investigated compounds. The values of ELF and LOL parameters for the selected bonds are small, which confirms the non-covalent character of these bonds in nature. The electronic spectra of the apalutamide drug, thymine and complex thymine/apalutamide in solvent water were calculated by Time Dependent Density Functional Theory(TD-DFT) for the investigation of interaction effect; Non-bonded interaction between the compound apalutamide and thymine has changed the value of λmax.     

Conformation of 1,2-Dimethoxyethane in Water

To understand the conformation of 1,2-dimethoxyethane (DME) in water, a system of two kinds of molecules, DME and H_2O, was focused. The interaction of various conformers of DME with water was studied by means of ab initio molecular orbital calculation with 6-31G (d) basis set. It is shown that there are two forms of interactions between the two molecules in the system, the close touched (H_2O attaches to the two oxygen atoms of DME) and the open touched (H_2O attaches to one oxygen atom of DME) structures. The conformation of DME is remarkably influenced by the interactions. Instead the ttt conformer is preferred in the gas state, with a close touched H_2O the tgt conformer becomes the most stable one. The obtained hydration energies show that the stabilized order of DME conformers by water is tgt>tgg′>ttt.     

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%.     

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.     

Synthesis and Crystal Structure of a New Dinuclear Manganese(Ⅱ) Manganese(Ⅲ) Complex of a Macrocyclic Ligand

A mixed-valence dinuclear manganese complex, [MnⅡMnⅢL](ClO4)·1/2MeOH, where L is a macrocyclic ligand derived from the cyclocondensation of sodium 2,6-diformyl-4-methylphenolate with N,N-bis(2-aminoethyl)-2-hydroxybenzyl amine, was obtained and its structure was determined by X-ray diffraction. The orange crystal is a monoclinic system with space group P21/c and lattice parameters a=1.1617(4), b=1.4005(3), c=1.4641(3) nm, β=113.03(2)°, and Z=2. The crystal structure shows that each pendant-arm is bonded in a bidentate fashion to the adjacent metal atom and that both the arms are on the same side of the macrocycle. The two Mn atoms are bridged by two μ2-phenoxy oxygen atoms of the tetra-imine macrocycle, and each Mn atom, locating in a trigonal prismatic coordination environment(N3O3), is six-coordinated by the two imine nitrogen atoms, one tertiary nitrogen atom and a pendant phenol moiety apart from the two oxygen atoms.     

REFINED CRYSTAL STRUCTURE OF INSULIN AT 1.8A RESOLUTION——HYDROGEN BONDS AND BOUND WATER

The hydrogen bonds in insulin fall into three cases: the helical hydrogen bonds in α- or 3_(10)helices, the non-helical one formed by polar groups of insulin itself, and the hydrogen bondsformed between insulin and water. By using the information obtained, the results of a seriesof biochemical investigations on insulin analogs related to B-chain C-terminal peptide can beinterpreted and it can also be inferred that the complex behaviours of the aggregation ofinsulin may play a protective role for the unique conformation of the molecule. Water structure also appears in the refined model. About one third of the water in anasymmetric unit is hydrogen-bonded to insulin molecules or each other, which are referred toas bound water. The polar and charged groups of insulin all show the tendencies to bind towater molecules as many as possible, which is a significant factor for the stabilization of theunique conformation of the molecule. The binding way of water molecules to insulin mole-cules is also analysed.     

A Three-dimensional Ba(Ⅱ) Coordination Polymer Based on H_4AQTC(Anthraquinone-1,4,5,8-tetracarboxylic Acid): Quinone Oxygen Atoms Participate in Coordination

A novel coordination polymer [Ba2(AQTC)(H2O)3]n(1, H4 AQTC = anthraquinone-1,4,5,8-tetracarboxylic acid) has been prepared under hydrothermal conditions and characterized by single-crystal X-ray diffraction, elemental analysis, infrared spectroscopy and thermogravimetric analysis. Two quinone oxygen atoms and all carboxylate oxygen atoms of AQTC4- are involved in coordination. Two equivalent barium ions are mainly linked by carboxylate oxygen atoms into a dimer. Neighbouring dimers are further connected by the AQTC4- ligand through carboxylate oxygen atom, leading to a 1-D chain structure. Every two adjacent chains are mainly further connected by face carboxylate oxygen atoms and water molecule, generating a two-dimensional layer structure. Such 2-D layer structures are connected with O(6) and O(6C) atoms from water molecules to form a 3-D structure. In addition, luminescent properties of 1 are also investigated.     

Ab initio Calculation of Intermolecular Dispersion Energy and Induction Energy of Nitramide Dimer

The dispersion energies, induction energies and their exchange counterparts (exchange-dispersion and exchange-induction energies) between two interacting nitramide molecules at several separations are derived based upon symmetry-adapted perturbation theory (SAPT). The results show that (1) the effect of intramonomer electron correlation on dispersion energies and induction energies for nitramide dimer system is remarkable especially in the region near the van der Waals minimum distance (0.42 nm). (2) At smaller separations the dispersion energies and the induction energies are largely quenched by their exchange counterparts, and this case in induction interaction is much more remarkable than in dispersion interaction. (3) Since at shorter distances there exists the strong short-range interaction due to electron transfer which quickly decays and even disappears at larger separations, the two different R-dependency formulae of induction energies were found: one is ca. R^-12.7 at short distances, and the other ca. R^-7.0 at large separations. The latter R-dependency is similar to that (ca.R^-7.2) of dispersion. (4) In the case of strong polar interaction existing in nitramide dimer, the “true“ induction correlation terms of higher order than ^1Eind^(22) may be important.     

THE SYNTHESIS AND CRYSTAL STRUCTURE OF A NOVEL TETRANUCLEAR COPPER (Ⅰ) CLUSTER COMPLEX, Cu_4(α-C_(10)H_7CSS_2)_4·1/2CS_2

The title compound has been synthesized by the reaction of sodium α-dithionaphthoatewith CuCl_2 in an alkaline aqueous solution or by the reaction of α-dithionaphthoic acid withCuCl_2 in an organic solvent, The crude product was recrystallized in a mixture of CS_2 andC_2H_5OH. The crystals obtained are red and stable in air. The structure of the title compound is determined by a single-crystal X-ray diffractionanalysis. The crystal belongs to monoclinic space group C_(2h)~5- P(2_1/a) with unit cell parameters:a= 16.453(3)A, b=12.651(4)A, c=23.182(7)A, β=100.5(2)°, V=4744.6A~3,Z=4. Thestructure was refined to R=0.06 for 4707 reflections. In the molecule, Cu_4 cluster has a distorted tetrahedral configuration. Surrounding thistetrahydron are four α-perthionaphthoate ligands, coordinated to copper through the sulfuratoms. One of the sulfur atoms in each ligand forms sulfur bridge with copper atoms,while the other is coordinated to only one copper. The three Cu--S bonds formed by thethree sulfur atoms with a given copper atom are approximately coplanar. Each group--C--S_2 with Cu atom on a vertex of the tetetrahedron forms a five-member ring. Thesefive-member rings are also approximately cooplanar. The molecule possesses an approachingS_4 point symmetry. The mechanism for the formation of the title compound involves a redox reaction.which is discussed in this paper.     

Solubilities of 1,2,3-trimethylbenzene and 1,2,4-trimethylbenzene and 1,3,5-trimethylbenzene in t-butyl alcohol+water mixtures and hydrophobic interaction

The solubilities of 1,2,3- trimethylbenzene, 1,2,4-trimethylbenzene and 1,3,5-trimethylbenzene in mixed solvents of t-butyl alcohol (TBA) and water at 283.15, 288.15, 293.15 and 298.15 K have been determined by spectrophotometry. The mole fractions of TBA [x(TBA)] in the mixed solvent are 0.000, 0.010, 0.020, 0.030, 0.040, 0.045, 0.050, 0.060, 0.080 and 0. 1000. The Gibbs energies of hydrophobie interaction (HI) for the aggregating process of three methane molecules with one benene molecule in the mixed solvent are studied, and the effect of solvent structure and solute aggregating state on the strength of HI is discussed.     

Hydrothermal Synthesis and Crystal Structure of a Novel Dinuclear Co(Ⅱ) Complex:[Co2(2,2'-bpy)_2(μ-L)_2(L)_2(μ-H_2O)](HL=4-Chlorobenzoic Acid)

A new 4-chlorobenzoic acid bridge Co(Ⅱ) complex [Co2(2,2'-bpy)2(μ-L)2(L)2(μ-H2O)] (HL=4-chlorobenzoic acid) has been obtained by hydrothermal synthesis,and X-ray single-crystal diffraction analysis shows that it crystallizes in the monoclinic system,space group C2/c with a=22.537(5),b=16.212(3),c=15.306(3) ,β=124.37(3)°,V=4616.1(16) 3,Mr=1070.45,Dc=1.540 g/cm3,Z=4,μ=1.012 mm-1,F(000)=2176,the final R=0.0338 and wR=0.0810. The title complex is composed of dinuclear [Co2(2,2'-bpy)2(μ-L)2(L)2(μ-H2O)] molecules. Each Co(Ⅱ) atom is coordinated by two nitrogen atoms from one 2,2'-bipyridine ligand,three oxygen atoms from three 4-chlorobenzoic ions and another oxygen atom from one water molecule. The two Co(Ⅱ) atoms are connected by two 4-chlorobenzoic ions and one bridged water molecule. The dinuclear molecules are interlinked by hydrogen bond and π-π stacking interactions into a three-dimensional supramolecular network.     

Hydrothermal Synthesis and Crystal Structure of a Novel Dinuclear Co(Ⅱ) Complex: [Co2(2,2(')-bpy)2((-L)2(L)2(μ-H2O)] (HL = 4-Chlorobenzoic Acid)

A new 4-chlorobenzoic acid bridge Co(Ⅱ) complex [Co2(2,2(')-bpy)2(μ-L)2(L)2(μ- H2O)] (HL = 4-chlorobenzoic acid) has been obtained by hydrothermal synthesis, and X-ray single-crystal diffraction analysis shows that it crystallizes in the monoclinic system, space group C2/c with a = 22.537(5), b = 16.212(3),c = 15.306(3)(A), β= 124.37(3)°, V = 4616.1(16) (A)3, Mr = 1070.45, Dc = 1.540 g/cm3, Z = 4, μ = 1.012 mm-1, F(000) = 2176, the final R = 0.0338 and Wr = 0.0810. The title complex is composed of dinuclear [Co2(2,2(')-bpy)2(μ-L)2(L)2(μ-H2O)] molecules. Each Co(Ⅱ) atom is coordinated by two nitrogen atoms from one 2,2'-bipyridine ligand, three oxygen atoms from three 4-chlorobenzoic ions and another oxygen atom from one water molecule. The two Co(Ⅱ) atoms are connected by two 4-chlorobenzoic ions and one bridged water molecule. The dinuclear molecules are interlinked by hydrogen bond and π-π stacking interactions into a three-dimensional supramolecular network.     

Hydrothermal Synthesis and Crystal Structure of a Novel Dinuclear Co（ Ⅱ ） Complex： [Co2（2,2＇-bpy）2（μ-L）e（L）2（μ-H2O）] （HL = 4-Chlorobenzoic Acid）

ABSTRACT A new 4-chlorobenzoic acid bridge Co（Ⅱ ） complex [[Co2（2,2＇-bpy）2（μ-L）e（L）2（μ-H2O）] （HL = 4-chlorobenzoic acid） has been obtained by hydrothermal synthesis, and X-ray single-crystal diffraction analysis shows that it crystallizes in the monoclinic system, space group C2/c with a = 22.537（5）, b = 16.212（3）, c = 15.306（3） A, β= 124.37（3）°, V= 4616.1（16）A3, Mr = 1070.45, Dc = 1.540 g/cm3, Z = 4, p = 1.012 mm-1, F（000） = 2176, the final R = 0.0338 and wR= 0.0810. The title complex is composed of dinuclear [Co2（2,2＇-bpy）2（μ-L）2（L）2（μ-HaO）] molecules. Each Co（Ⅱ ） atom is coordinated by two nitrogen atoms from one 2,2’-bipyridine ligand, three oxygen atoms from three 4-chlorobenzoic ions and another oxygen atom from one water molecule. The two Co（Ⅱ） atoms are connected by two 4-chlorobenzoic ions and one bridged water molecule. The dinuclear molecules are interlinked by hydrogen bond and π-π stacking interactions into a three-dimensional supramolecular network.     

Synthesis,Crystal Structure and Thermal Stability Properties of a Binuclear Copper(Ⅱ) Coordination Polymer {[Cu_2(4,4'-bipy)_2(o-ABA)_4(H_2O)_2][(H_2O)_2]}_n

One-dimensional chain copper(Ⅱ) coordination polymer has been synthesized and characterized in the solvent mixture of water and alcohol with o-acetamidobenzoic acid,4,4'-bipyridine and copper perchlorate.It is of tetragonal,space group P41212 with a=1.57756(10),b= 1.57756(10),c=2.1438(3)nm,V=5.3352(8) nm3,Dc=1.524 g/cm3,Z=4,F(000)=2536,R= 0.0479 and wR=0.0979.The crystal structure shows two coordination modes.The copper(1) is coordinated with two nitrogen atoms of one 4,4'-bipyridine molecule and two oxygen atoms from two o-acetamidobenzoic acid molecules,forming a distorted tetrahedral coordination geometry;the copper(2) is coordinated with two nitrogen atoms of one 4,4'-bipyridine molecule,four oxygen atoms from two o-acetamidobenzoic acid molecules and two water molecules,generating a distorted octahedral coordination geometry.The result of TG analysis shows that the title complex is stable below 180.0 ℃.     

CRYSTAL STRUCTURES OF COPPER (Ⅱ) AND COBALT (Ⅲ) COM- PLEXES OF o-HYDROXYBENZYLGLYCINATE (HBG)

<正> The structures of two complexes C(CuOC6H4CH2NHCH2COO)2 (H2 O)]·H2P(1) and [Co(NH3)6[Co(OC6H4CH2NHCH2COO)2]2[C1]·10H2O (2) were determined by X-ray analyses. Compound (1) crystallizes in the orthorhombic space group P212121 with a=11. 357(1),b= 24. 304(2),c=7.317(4) A,Z= 4;While compound (2) in the monoclinic space group A2/a(C2/c) with a=23. 486(9) ,b=26. 605(6) ,c= 10. 542(1) A,γ= 128. 42(4)°,Z= 4. In compound (1),two Cu(Ⅱ) ions are bonded together by the phenolic oxygen atoms of two tridentate chelating ligands and each of them is separately coordinated by the carboxyl oxygen,amino nitrogen of each chelate ligand and by the fifth oxygen atom as well (from aqua or the carbonyl group in adjacent molecule). Thus the coordination of each Cu(Ⅱ) is a square pyramid with distances of 1. 93- 1. 97A to the four corner atoms and 2. 30 and 2. 32 A to the apex atoms. The whole molecule has an approximately planar configuratioir with the two pyramid apexes pointing towards one side. Compound (2) consists of     

DFT Study on Molecule C20H10:Five Carbon-carbon Single Bonds Linking Two Pentaprismane Cages

1 INTRODUCTION In recent years, a great number of achievements have been achieved in the field of molecules with cage-like structures, such as fullerenes and poly- hedral hydrocarbons. Each of these molecules has only one cage, such as C60 and dodecahedrane. As is well known, every carbon atom can form four single bonds with other atoms. Since each carbon atom at the cage surface of the carbo-polyhedral molecule only forms three bonds with other carbon atoms, it may form the fourth singl…     

Cytosinium Isophthalate: Crystal Structure Redetermination and Room Temperature Phosphorescence

The title compound cytosinium isophthalate(C-H_2IA) self-assembly of cytosine(C) and isophthalic acid(H_2IA) in aqueous media has been synthesized and the crystal structure with a reasonable protonation state is redetermined. Single-crystal X-ray diffraction analysis reveals that each asymmetric unit contains one protoned cytosine molecule and one deprotoned isophthalic acid. The proton transferred from carboxylic acid to the pyrimidine ring is disordered across an inversion center with occupancy of 0.5 and the proton located to one of the carboxylate group lies on an inversion center shared by two crystallographically equivalent oxygen atoms. In addition, the cytosine molecules are connected by complementary hydrogen bonds to form a one-dimensional tape structure. The neighboring isophthalic acids are connected via hydrogen bonds between carboxyl groups to form a one-dimensional lattice like tape. Furthermore, the adjacent organic base tapes and organic acid tapes are stacked one with another through π-π stacking interactions to form a three-dimensional supramolecular structure. Interestingly, C-H_2IA displays a green phosphorescence in solid state at room temperature with the lifetime of 0.7 s determined by time resolved studies, indicating that supramolecular C-H_2IA is a potential pure organic phosphorescent luminogens.     

WATER STRUCTURE IN DESPENTAPEPTIDE (B26—B30) INSULIN CRYSTAL AT 1.5  RESOLUTION

The water structure in despentapeptide (B26-B30) insulin crystal is presented in this paper. Ac-cording to inspection of the final F_0-extended (2F_0-F_c) Fourier map, 81 water molecules (about twothirds of solvent) with electron density greater tLan 0.4 e/A~3 are included in the water model to bediscussed. In a hydrogen bond length range of 2.4--3.2 A, 51 water molecules, that is, 63% of thetotal 81, are hydrogen bonded to protein, of which 12 link the adjacent protein molecules through one-water bridges and more through two-water bridges. There is a tight water network in a long crevice be-tween protein molecules; two Cd atoms, like two piles, prop up the network through three water molecules(Cd ligands) at either end of the network, indicating that Cd ions and water networks play an importantrole in close packing of protein molecules in the crystal.