A MOLECULAR ORBITAL STUDY ON ADENOSINE PHOSPHATES

AMP, ADP and ATP are calculated using the CNDO method, and ATP is studied by an ab initio calculation.The essential features of the electronic structure of these molecules are described in detail. Their ionization potentials, dipole moments and bond orders are given.The interaction between ATP with metal ions and enzyme molecules is discussed.     

Theoretical Investigation on Interaction between Guanine and Luteolin

The interacting patterns of the luteolin and guanine have been investigated by using the density functional theory B3LYP method with 6-31＋G＊ basis set. Eighteen stable structures for the luteolin-guanine complexes have been found respectively. The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions. Meanwhile, both the number and strength of hydrogen bond play important roles in determining the stability of the complexes which can form two or more hydrogen bonds. Theories of atoms in molecules and natural bond orbital have also been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes which were corrected by basis set superposition error are 6.04-56.94 kJ/mol. The calculation results indicate that there are strong hydrogen bonding interactions in the luteolin-guanine complexes. We compared the interaction between luteolin and four bases of DNA, and found luteolin-thymine was the strongest and luteolin-adenine was the weakest. The interaction between luteolin and DNA bases are all stronger than luteolin-water.     

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.     

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,     

Strength of Intramolecular Hydrogen Bonds

The concept of resonance-assisted hydrogen bonds(RAHBs)highlights the synergistic interplay between theπ-resonance and hydrogen bonding interactions.This concept has been well-accepted in academia and is widely used in practice.However,it has been argued that the seemingly enhanced intramolecular hydrogen bonding(IMHB)in unsaturated compounds may simply be a result of the constraints imposed by theσ-skeleton framework.Thus,it is crucial to estimate the strength of IMHBs.In this work,we used two approaches to probe the resonance effect and estimate the strength of the IMHBs in the two exemplary cases of the enol forms of acetylacetone and o-hydroxyacetophenone.One approach is the block-localized wavefunction(BLW)method,which is a variant of the ab initio valence bond(VB)theory.Using this approach,it is possible to derive the geometries and energetics with resonance shut down.The other approach is Edmiston’s truncated localized molecular orbital(TLMO)technique,which monitors the energy changes by removing the delocalization tails from localized molecular orbitals.The integrated BLW and TLMO studies confirmed that the hydrogen bonding in these two molecules is indeed enhanced byπ-resonance,and that this enhancement is not a result ofσconstraints.     

Structure of cis-[Pt(NH_3)(2-picoline)]~(2+) and DNA adduct and its bonding characteristics

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DMA segment d(ATACATG*G*TACATA)-d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.     

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.     

Nature of the Ga-Ga bonding in Na2[Arx*GaGaArx*]（Arx*=C6H3 -2,6-（C6H5）2）:Electron localization function analysis

The nature of the Ga-Ga bonding in Na2[Arx*GaGaArx*](Arx* = C6H3-2,6-(C6H5)2) has been investigated and compared with that of in H2[Arx*GaGaArx*] using electron localization function(ELF) and orbital analysis.The calculation results show that in Na2[Arx*GaGaArx*],the Ga-Ga interaction is a non-classical triple bond,the heart of Na2[Arx*GaGaArx*] is the Ga2Na2 cluster rather than a simple Ga-Ga bond,and the contribution of the sodium atoms to the short Ga-Ga bond length is considerable.As the two sodium atoms are substituted by two hydrogen atoms,the Ga-Ga bond is replaced by two 3-center,2-electron(3c-2e) Ga-H-Ga covalent bridged bonding.     

Aminolysis reaction of calix [ 4 ] arene esters and crystal structures and conformational behaviors of calix[4]arene amides

We first make use of aminolysis of calix[4]arene esters to synthesize calix[4]arene amides. When the two ethyl esters of the calix[4]arene esters are aminolysized, the 1, 3-amide derivative is formed selectively. The crystal structures of the calix-[4]arene with two butyl amide (3b) and four butyl amide moieties (4b) were determined. The intermolecular hydrogen bonds make 4b form two-dimensional net work insolid state. The 1H NMR spectra prove that 3b is of a pinched cone conformation, while 4b and tetraheptylamide-calix[4]arene (6b) take fast interconversion between two C2v isomers in solution and appear an apparent cone conformation at room temperature. As decreasing temperature, the interconversion rate decreases gradually and, finally, the interconversion process is frozen at Tc = -10℃, which makes both conformations of 4b and 6b the pinched cone structures. The hydrogen bond improves the interconversion barrier, and the large different values of the potential barrier between 6b and 4b (or 6b) may     

Molecular mechanics study on conformation of perylene-quinonoid photosensitizers

Using molecular mechanics method,values of the heat of formation (HF) of different conformations,of perylenequinonoid photosensitizes hypocrellin A (HA) and hypocrellin B (HB) were calculated and the variance of HF after phenolic protons' dissociation were calculated as well The following was found:(i) The HF values of lour conformational isomers of HA and HB are similar to each other,so the four isomcrs can transform to each other room temperature,(ii) There exists the difference between the ability of dissociation of phenolic protons of HA and that of HB,the former is higher than the latter (iii) There exist two intramolecular hydrogen bonds in HA and HB The bond energy is approximately 8 kJ/mol and the energy of conformation Ⅰ is lower than that of conformationⅡ The bond energy of HA is lower than that of HB.(iv) There exists a low energy snot when phenolic hydroxyl bond twists 180° from the position where hydrogen bond is formed,which suggests that this kind of conformation probably exists,(v) Th     

CLOUD POINT CURVES OF POLY(ETHYLENE GLYCOL)/POLY(PROPYLENE GLYCOL) MIXTURES AND THEIR THERMODYNAMIC EXPLANATION

In the study of poly(ethylene glycol) (PEG) and poly(propylene glycol) (PPG) mixtures not only a bimodal shape but also a reverse trend of the dependence on molecular weight of the cloud point curves were observed.This trend indicates that the miscibility of the studied mixtures decreases as the molecular weight of one component decreases. The excess volumes of the mixtures show that the interaction parameter between two components decreases at first and increases after passing a minimum as the concentration of one component increases. This supports the explanation of Koningsveld on the bimodal shape of cloud point curves. Based on a binary interaction model a formula was derived revealing that the interaction between PPG and the end group of PEG and the hydrogen bonding interaction between ether and hydroxy end group inner or inter PEG molecules are not favorable for mixing. The latter interaction is an "attractive" force in PEG molecules. The two interactions are responsible for the observed abnormal dependence.     

Pyrrolic Amide: A New Hydrogen Bond Building Block for Self-assembly

Molecular self-assembly has emerged as a powerful technology for the synthesis of nanostructured materials. In design of various molecular assemblies, hydrogen bonding is a preferably selected intra- or inter-molecular weak interaction in recent research by virtue of the directionality and specificity. The research for novel hydrogen bond building blocks that self-assembly into well defined structures is great important not only for gaining an understanding of the concepts of self-assembly but also for the design of new molecular materials. Pyrrolic amide moiety has one hydrogen bond acceptor (C =O) and two hydrogen bond donors (pyrrole NH and amide NH). By deliberately design, pyrrolic amide compounds would be new kinds hydrogen bond building blocks. So, pyrrolic amide compounds 1 ～ 6, which bear one, two or three pyrrolic amide moieties respectively, were designed and synthesized.     

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.     

On the accuracy of the potential harmonic functions

The matrix elements of the correlation function between symmetric potential harmonics are simplified into the analytical summations of the grand angular momenta by smartly using the recurrence and coupling relations of the potential harmonics. The correlation-function potential-harmonic and generalized-Laguerre-function method (CFPHGLF) , recently developed by us, is applied to the S states of the helium-like systems for Z = 2 to 9. The results exhibit good convergence with the bases in terms of both the angular and radial directions. The final eigen-energies agree excellently with the best s-limits of the variational configuration interaction (CI) method for the involved low-lying S states. The accuracy of the potential harmonic (PH) expansion scheme is discussed relative to the exact Hylleraas CI results (HCI), and Hartree-Fock results. Moreover, suggestion is given for the future improvement of the PH scheme.     

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.     

The open-close mechanism of M2 channel protein in influenza A virus:A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41

The M2 protein from influenza A virus is a tetrameric ion channel. It was reported that the permeation of the ion channel is correlated with the hydrogen bond network among His37 residues and the cation-π interactions between His37 and Trp41. In the present study,the hydrogen bonding network of 4-methyl-imidazoles was built to mimic the hydrogen bonds between His37 residues,and the cation-π interactions between 4-methyl-imidazolium and indole systems were selected to represent the interac-tions between His37 and Trp41. Then,quantum chemistry calculations at the MP2/6-311G level were carried out to explore the properties of the hydrogen bonds and the cation-π interactions. The calcula-tion results indicate that the binding strength of the N-H···N hydrogen bond between imidazole rings is up to -6.22 kcal·mol-1,and the binding strength of the strongest cation-π interaction is up to -18.8 kcal·mol-1(T-shaped interaction) or -12.3 kcal·mol-1(parallel stacking interaction). Thus,the calcu-lated binding energies indicate that it is possible to control the permeation of the M2 ion channel through the hydrogen bond network and the cation-π interactions by altering the pH values.     

Syntheses, Crystal Structures and Photoluminescence Properties of Cadmium(Ⅱ) and Nickel(Ⅱ) Complexes with 2-(2-Benzimidazolyl)quinoline

Two novel complexes, [Cd2(BMQU)2Cl4] (1) and [Ni(BMQU)2HPO4]·1.5H2O (2) (BMQU = 2-(2-benzimidazolyl)quinoline), were synthesized by the hydrothermal method and characterized by elemental analysis, IR, and TG-DTG. The crystal structures were determined by single-crystal X-ray diffraction. Both 1 and 2 crystallize in the triclinic system, space group P . The data for 1: a = 0.8342(7), b = 0.9226(9), c = 1.0646(8) nm, α = 90.819(2), β = 97.466(2), γ = 98.280(2)°. The Cd(Ⅱ) is coordinated with three chlorine atoms and two nitrogen atoms of a BMQU molecule, generating a distorted square-pyramidal geometry. The dinuclear Cd(Ⅱ) complex is formed by two chlorine bridge bonds, and the one-dimensional chain structure is constructed with the hydrogen bond N-H…Cl and π-π stacking interaction. The data for 2: a = 1.2251(1), b = 1.2451(1), c = 1.2868(1) nm, α = 107.510(2), β = 98.630(1), γ = 109.921(2)°. The Ni(Ⅱ) is coordinated with four nitrogen atoms of two BMQU molecules and two oxygen atoms of a HPO42-, forming a distorted-octahedral geometry. The two-dimensional layer structure is formed by the hydrogen bonds and π-π stacking interaction between neighboring molecules. Complex 1 shows a strong blue fluorescence emission (λmax= 456 nm) at solid state.     

Microcrystal induced emission enhancement of a small molecule probe and its use for highly efficient detection of 2,4,6-trinitrophenol in water

In this contribution, we reported a very simple and small molecule material, 2,5-dimethoxyterephthalaldehyde(DMA). It exhibited a relatively weak fluorescence in solution, while showed a steadily increased green fluorescence with typical aggregation-induced enhanced emission(AIE) effect for forming a cubic-like microcrystal structure in THF-H2 O mixed solvent.The microcrystals presented significantly higher fluorescence than that of amorphous aggregates. The DMA microcrystals suspension showed a good response to 2,4,6-trinitrophenol(TNP) with a LOD of 1.2×10~(-7) M, which is the best result of TNP detection in aqueous solution. Quantum chemical calculation revealed that DMA is a donor(D)-receptor(A) type molecule with methoxy unit as donor and carbonyl moiety as receptor. Its emission arises from an intramolecular charge transfer(ICT) from methoxy units to carbonyl units. NMR indicated that there is a strong hydrogen bond interaction between DMA and TNP.Hydrogen bond interaction can effectively decrease the intermolecular distance of DMA and TNP, which will increase the efficiency of photoinduced electron transfer(PET) and fluorescence resonance energy transfer(FRET), and hence will be advantageous for its selectivity. The microcrystal induced enhanced emission could be generally used for kinds of target molecules analysis.     

An SCF-CI method for determining the potential energy surface of a triatomic molecule

A self-consistent-field (SCF)-configuration interaction (CI) (SCF-CI) method for determining the potential energy surface of a triatomic molecule from the observed vibrational band origins has been suggested. By this method, the SCF-CI procedure in the internal coordinates is used to calculate the vibrational bond origins and their first derivatives with respect to parameters in the potential energy function using the exact vibrational Hamiltonian, and the optimizer LMF in the nonlinear-squares problem is employed to optimize parameters in the potential energy function. This approach is used to optimize the potential energy function of the water molecule. The standard deviation of this fitting to the 70 observed band origins is 1.154cm-1.     

Molecular Recognition of Pyromellitic Imide-azacyclophane to Organic Pollutant

Anion can be identified by pyromellitic imide-azacyclophane which is one of the host compounds.This article investigated the interaction between the host and organic pollution compounds.The host and other eight compounds were optimized by DFT(density functional theory) B3LYP/6-31G level and the energy of compounds was corrected using Boys-Bemardi method.On the basis of B3LYP/6-31G optimized geometries,the RDG function and sign(λ2(r))ρ(r) function values of space points were calculated,and color RDG isosurface map was drawn.3He chemical shift was calculated by the B3LYP/6-31G method.The results showed that the eight organic pollution molecules with the host one shaped stable configurations by hydrogen bonds,respectively.The stabilization energy of complexes 4 and 7 showed repulsion(steric effects) of cyclophane cage observably affecting the stability of the complexes.The location,intensity and the type of interaction in complex 1 were analyzed through color-filled RDG isosurface map.Aromaticity calculations showed that the weak interaction reduced the transverse induction ring current in the host rings,and deteriorated the aromaticity of compounds.