Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C_nmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH₂O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH₂O-y[C_nmim]⁺-xBr⁻, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H₂O-Br⁻-1, T-3H₂O-[C_nmim]⁺-Br⁻-1, T-2H₂O-[C_nmim]⁺-2Br⁻-1, and T-1H₂O-2[C_nmim]⁺-2Br⁻-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C_nmim]⁺) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br⁻) is front > top. The stability order for the different microhydrates is following T-5H₂O-1 < T-4H₂O-Br⁻-1 < T-3H₂O-[C_nmim]⁺-Br⁻-1 < T-2H₂O-[C_nmim]⁺-2Br⁻-1 < T-1H₂O-2[C_nmim]⁺-2Br⁻-1. A good linear relationship between binding E_B values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π⁺ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C_nmim]⁺ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr⁻ complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.     

Cooperative enhancement of water binding to antiparallel β‐sheet models: Analysis by ab initio calculations

The cooperative enhancement of water binding to the antiparallel β‐sheet models has been studied by quantum chemical calculations at the MP2/6‐311++G**//MP2/6‐31G* level. The binding energies of the two antiparallel β‐sheet models consisting of two strands of diglypeptide are calculated by supermolecular approach. Then water molecules are gradually bonded to the diglypeptide by N? H···OH₂ and C?O···HOH hydrogen bonds. Our calculation results indicated that the hydrogen bond length and the atom charge distribution are affected by the addition of H₂O molecules. The binding energy of antiparallel diglypeptide β‐sheet models has a great improvement by the increasing of the hydrogen bond cooperativity and the more H₂O molecules added the more cooperativity enhancement can be found. The orbital interactions are calculated by natural bond orbital analysis, and the results indicate that the cooperative enhancement is closely related to the orbital interaction. © 2012 Wiley Periodicals, Inc.     

DFT study on cooperativity in the interactions of hydrazoic acid clusters

Density functional theory at the B3LYP level with the 6‐311G** basis set is performed to calculate the systems consisting of up to four hydrazoic acid molecules. The dimers are found to exhibit cyclic and chain structures with N … H contacts at ca. 2.1–2.7 Å. However, there are only cyclic structures with N … H contacts at ca. 2.0–2.3 Å and 2.0–2.1 Å in the trimer and tetramer, respectively. Hydrogen bond distances in the trimer and tetramer are shorter than those in the cyclic dimer as a result of the stronger interaction between molecules. The contribution of cooperative effect to the interaction energy is significant. After the correction of the basis set superposition error and zero‐point energy, the binding energies are ?10.69, ?29.34, and ?54.26 kJ·mol^?1 for the most stable dimer, trimer, and tetramer, respectively. The calculated IR shifts for N? H stretching mode increase with the size of the cluster growths, reaching more than 200 cm^?1 in the tetramer. For the most stable clusters, the transition from the monomer to dimer, dimer to trimer, and trimer to tetramer involve changes of ?14.40, ?25.68, and ?31.88 kJ·mol^?1 for the enthalpies at 298.15 K and 1atm, respectively. We also perform Mulliken populations analysis and find the Mulliken populations on intermolecular N … H increasing in the sequence of the dimer, trimer, and tetramer. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 279–286, 2003     

Ab initio study of the structure,cooperativity, and vibrational properties in the mixed hydrogen‐bonded trimers of hydrogen isocyanide and water

The five trimers of H₂O···HNC···H₂O, H₂O···H₂O···HNC, HNC···H₂O···H₂O, H₂O···HNC···HNC, and HNC···HNC···H₂O have been studied with quantum chemical calculations. Their structures, harmonic vibrational frequencies and interaction energies have been calculated at the B3LYP and MP2 levels with the aug‐cc‐pVDZ and aug‐cc‐pVTZ basis sets. The cooperative effect on these properties has also been studied quantitatively. For HNC:(H₂O)₂ systems, the cyclic H₂O···H₂O···HNC trimer is most stable with an interaction energy of ?16.01 kcal/mol and a large cooperative energy of ?3.25 kcal/mol at the MP2/aug‐cc‐pVTZ level. For H₂O:(HNC)₂ systems, the interaction energy and cooperative energy in the H₂O···HNC···HNC trimer are larger than those in the HNC···HNC···H₂O trimer. The NH stretch frequency has a blue shift for the terminal HNC molecule in the HNC···H₂O···H₂O and HNC···HNC···H₂O trimers and a red shift in other cases. A many‐body analysis has also been performed to understand the interaction energies in these hydrogen‐bonded clusters. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A Binary Bivalent Supramolecular Assembly Platform Based on Cucurbit[8]uril and Dimeric Adapter Protein 14-3-3

Interactions between proteins frequently involve recognition sequences based on multivalent binding events. Dimeric 14-3-3 adapter proteins are a prominent example and typically bind partner proteins in a phosphorylation-dependent mono- or bivalent manner. Herein we describe the development of a cucurbit[8]uril (Q8)-based supramolecular system, which in conjunction with the 14-3-3 protein dimer acts as a binary and bivalent protein assembly platform. We fused the phenylalanine–glycine–glycine (FGG) tripeptide motif to the N-terminus of the 14-3-3-binding epitope of the estrogen receptor α (ERα) for selective binding to Q8. Q8-induced dimerization of the ERα epitope augmented its affinity towards 14-3-3 through a binary bivalent binding mode. The crystal structure of the Q8-induced ternary complex revealed molecular insight into the multiple supramolecular interactions between the protein, the peptide, and Q8.     

竞争还是协同：分子内两类磷键Sb---X(X=O、N、F)和Sb---π的关系

本文通过选取多个双官能团有机分子(甲氧基甲基苯(1)、苄基二甲胺(2)、氟甲基苯(3))和无机分子SbCl₃,利用密度泛函理论详细考察了两类分子内磷键,Sb---X(X=O、N、F)与Sb---π之间的作用关系。研究结果表明,分子内均存在两种作用,并且二者是竞争关系,不存在协同性。分子1、2、3的结合能依次为-14.0、-17.0、-9.0 kcal mol^_-1。对于1,结合以Sb---O键为主,Sb---π为辅;对于2,结合基本均来自于Sb---N作用;而对于3,结合则以Sb---π作用为主。该结果体现了相互作用随原子序数的渐变性,为通过磷键调控体系的性质提供了理论依据。     

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase

Summary R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central active-site pore. Two reactants (dihydrofolate, DHF), two cofactors (NADPH) or one of each (R67•DHF•NADPH) can be found simultaneously within the active site, the last one being the reactive ternary complex. As the positioning of the ligands has proven elusive to empirical determination, we addressed the problem from a theoretical perspective. Several potential structures of the ternary complex were generated using the docking programs AutoDock and FlexX. The variability among the final poses, many of which conformed to experimental data, prompted us to perform a comparative scoring analysis and molecular dynamics simulations to assess the stability of the complexes. Analysis of ligand–ligand and ligand–protein interactions along the 4 ns trajectories of eight different structures allowed us to identify important inter-ligand contacts and key protein residues. Our results, combined with published empirical data, clearly suggest that multipe binding modes of the ligands are possible within R67 DHFR. While the pterin ring of DHF and the nicotinamide ring of NADPH assume a stacked endo-conformation at the centre of the pore, probably assisted by V66, Q67 and I68, the tails of the molecules extend towards opposite ends of the cavity, adopting multiple configurations in a solvent rich-environment where hydrogen-bond interactions with K32 and Y69 may play important roles.     

Calorimetric and spin-label ESR studies of PEG:2000-DPPE containing DPPC/lyso-PPC mixtures

The thermotropic behavior of dipalmitoylphosphatidylcholine (DPPC) multibilayers containing up to 10 mol% of lyso-palmitoylphosphatidylcholine (lyso-PPC) with and without low content of poly(ethylene glycol:2000)-grafted dipalmitoylphosphatidylethanolamine (PEG:2000-DPPE) has been studied by high sensitivity differential scanning calorimetry (DSC) and electron spin resonance (ESR) using the spin probe di-tert-butyl-nitroxide (DTBN). The three lipids, dispersed in buffer at appropriate concentrations, form thermosensitive liposomes used as site-specific drug-delivery systems. Without polymer–lipids, the DPPC main transition temperature is downshifted of 1.2–1.3 °C at the highest lyso-PPC content. The molar enthalpy and the cooperative unit of the DPPC main transition first decrease rapidly, then more slowly and finally slightly increase with lyso-PPC content. Moreover, in the mixed dispersions, the membrane fluidity increases at any temperature. The addition up to 5 mol% of PEG:2000-DPPE to DPPC/10 mol% lyso-PPC mixtures does not affect neither the thermotropic phase behavior nor the transition cooperativity and the fluidity of the dispersions.     

Theoretical Studies on the Stabilities and Hydrogen Bond Actions of （H2O）n Clusters

1 INTRODUCTION In the latest ten years, the structure and function of water clusters have captured the interest of chemists. One of the most important study objects in water cluster is to describe the behavior of water so- lution quantitatively at molecule level, which will pave the way for the solving of some environmental and other scientific problems, such as the formation of acid rain and nucleation mechanism of little water drop. Besides, weak interaction in water clusters could be al…