Theoretical studies of complexes between Hg(II) ions and l‐cysteinate amino acids

In this study, ab initio and density functional theory methods have been used to understand the structures and thermodynamic stabilities of complexes formed between l ‐cysteine and mercury (II) ions in neutral aqueous solution. To better understand the interaction between sulfur and mercury (II) ion, the MP2, B3LYP, M06‐2X, and TPSS methods have been used to optimize [HgSH_x]^2?x, x = 1–4, complexes and compared to benchmark QCISD(T) structures. Furthermore, energies from these same methods are compared to CCSD(T)/CBS(2,3) energies. From these benchmark calculations, the M06‐2X method was selected to optimize l ‐cysteinate‐Hg(II) complexes and the MP2 method for estimating complex energies. l ‐cysteinate‐mercury (II) ion complexes are formed primarily by forming a bond between cysteinate sulfur and the mercury ion. Stable complexes of l ‐cysteinate and mercury can be formed in 1:1, 2:1, 3:1, and 4:1 ratios. Each complex is stabilized further by interaction between carboxylate oxygen and mercury as well as hydrogen bonding among complex cysteinate ligands. The results indicate that at high cysteinate to Hg(II) ratios high‐coordinate complexes can be present but at lower ratios the 2:1 complex should be dominant. © 2013 Wiley Periodicals, Inc.     

Theoretical investigation on charge‐assisted halogen bonding interactions in the complexes of bromocarbons with some anions

A series of dimeric complexes formed between bromocarbon molecules and two anions (Br^? and CN^?) have been investigated by using MP2 method. The quantum theory of atoms in molecules (QTAIM) and the second‐order perturbation natural bond orbital (NBO) approaches were applied to analyze the electron density distributions of these complexes and to explore the nature of charge‐assisted halogen bonding interactions. As anticipated, these interactions are significantly stronger relative to the corresponding neutral ones. The results derived from ab initio calculations described herein reveal a major contribution from the electrostatic interaction on the stability of the systems considered. Beside the electrostatic interaction, the charge‐transfer force and the second‐order orbital interaction also play an important role in the formation of the complexes, as a NBO analysis suggested. The presence of halogen bonds in the complexes has been identified in terms of the QTAIM methodology, and several linear relationships have been established to provide more insight into charge‐assisted halogen bonding interactions. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical studies on relation among structures,electric structures and magnetic interactions in MMX complexes

The electronic structures of Ni₂(dta)₄I and Pt₂(dta)₂I complexes were examined by using UB3LYP calculations in terms of relation between magnetic interactions and structures of those complexes. The calculated effective exchange integrals (J_ab) values by using experimental structures were −488 and −1274 cm⁻¹ for Ni₂(dta)₄I and Pt₂(dta)₄I complexes, respectively. Natural orbital (NO) analyses revealed the origin of the difference in their antiferromagnetic interactions. In order to explain a variety of structural phases in those complexes, such as averaged valence (AV), spin density wave (SDW), charge polarization (CP) and alternate charge polarization (ACP), potential and J_ab surfaces were also investigated. The calculated potential surfaces explained experimental results that Ni₂(dta)₄I complex only took AVSDW phase, while Pt₂(dta)₄I complex underwent AVSDW, CP and ACP phases by temperature.     

Emission spectra studies on the hydrogen-bonding complexes between p-methoxy-2-styrylquinoline and acids

The ground and excited state interactions between p-methoxy-2-styrylquinoline (2-StQ-OMe) and different protic acids with various acid concentrations were studied in different media. Emission bands due to the hydrogen bonding complex, protonation complex and aggregation or solid complex were observed for the first time, in n-hexane. The different reaction pathways were controlled by the solvent polarity and the concentrations of the protic acid. The acidity of acid was also important to the acid-base complex.     

Theoretical studies of [n]paracyclophanes and their valence isomers

Summary The valence isomerisations of benzene, [6]- and [7]paracyclophane to their Dewar benzene and prismane isomers are studied with the MNDO method using the unrestricted Hartree-Fock (UHF) and the configuration interaction (C.I.) approximations. The enthalpy of the reaction Dewar benzene benzene is H° _r =–68.9 kcal/mol and the activation enthalpy is H°=27.9 kcal/mol (with C.I.). The reaction path hasC _2v symmetry.The determination of several points of the lowest potential energy surface of [6]- and [7]paracyclophanes leads to a minimum reaction path having the same topology as for the potential energy surface of the nonbridged benzene. The only difference is a quantitative change in the energy values of the aromatic isomers due to the deformation introduced by the alkyl chain. For [6]paracyclophane, the activation enthalpy is H°=24.6 kcal/mol and the activation entropy is S ⁰=0.6 cal K^–1 mol^–1 calculated with C.I.The enthalpy of the reaction prismane Dewar benzene is H° _r –32 kcal/mol and the activation enthalpy is H°19 kcal/mol. The highest molecular symmetry group common to both molecules isC _2v , whereas the symmetry group of the reaction path is lowered toC _s . Along this reaction path is located a biradicaloid intermediate, separated by low activation barriers from the products. No significant changes of the potential energy surfaces are found for the bridged [n]prismanes and the [n]Dewar benzenes.All the calculated values, reaction enthalpies, activation enthalpies and entropies, are in a good agreement with literature experimental data.This article is dedicated to Professor A. Pullman     

Theoretical studies on di- and tetra-nuclear Ni pivalate complexes

A combination of DFT calculations and magnetic studies allow structural features of di- and tetra-nuclear nickel pivalate cage complexes to be deduced.     

Synthetic studies on neomarinone: practical and efficient stereoselective synthesis of the side chain

A practical and efficient stereoselective synthesis of the side chain of neomarinone is reported. The synthesis was achieved in six steps (41% overall yield) from 2-methyl-2-cyclohexenone. The key step is a novel stereoselective 1,4-conjugate addition/enolate alkylation by an epoxide-opening reaction.     

Cation-pi interactions with a model for the side chain of tryptophan: structures and absolute binding energies of alkali metal cation-indole complexes

Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.     

Non-covalent interactions between unsolvated peptides: helical complexes based on acid-base interactions

We have used ion-mobility mass spectrometry to examine the conformations of the protonated complex formed between AcA(7)KA(6)KK and AcEA(7)EA(7), helical alanine-based peptides that incorporate glutamic acid (E) and lysine (K). Designed interactions between the acidic E and basic K residues help to stabilize the complex, which is generated by electrospray and studied in the gas phase. There are two main conformations: (1) a coaxial linear arrangement where the helices are tethered together by an EKK interaction between the pair of lysines at the C-terminus of the AcA(7)KA(6)KK peptide and a glutamic acid at the N-terminus of the AcEA(7)EA(7) peptide and (2) a coiled-coil arrangement with side-by-side antiparallel helices where there is an additional EK interaction between the E and K residues in the middle of the helices. The coiled-coil opens up to the coaxial linear structure as the temperature is raised. Entropy and enthalpy changes for the opening of the coiled-coil were derived from the measurements. The enthalpy change indicates that the interaction between the E and K residues in the middle of the helices is a weak neutral hydrogen bond. The EKK interaction is significantly stronger.     

Theoretical studies on magnetic interactions between Cu(II) ions in salen nucleobases

The magnetic and other physical properties between Cu²⁺ ions coordinated by salen–base pairs (Cu²⁺–DNA) are examined by using DFT calculations. In order to consider effects of entanglement and dis-entanglement of the double helix chain, three types of structural disorders i.e. distance, rotation angle and discrepancy in XY-plane, are changed in the model dimer structure. All calculated results show that J_ab values are weak anti-ferromagnetic couplings. It is also found that the J_ab values strongly depend on the salen structure.     

Palladium carbonyl complexes with anions of N-heterocyclic carboxylic and pyridine-2-sulfonic acids

Synthesis, spectral characteristics, and structure of palladium(I) carbonyl complexes containing anions of N-heterocyclic carboxylic acids and pyridine-2-sulfonic acid of the general formula [Pd(CO)(NHC-CO₂)]n/[Pd(CO)(NHC-SO₃)]n, where NHC is an N-heterocycle, were described. The resulting complexes can be attributed to a binuclear structure with bridging or terminal coordination of carbonyl ligands depending on the nature of the substituents in the heterocycle.

     

Synthetic studies on the trans-chlorocyclopropane dienyne side chain of callipeltoside A

[structure] Enantiomerically enriched trans-chlorocyclopropanemethanol was obtained by lipase kinetic resolution of dichlorocyclopropanemethanol 3, followed by reduction. The sp-sp(2) bond of the trans-chlorocyclopropane dienyne side chain of callipeltoside A was constructed via a Stille coupling reaction of 1, 1-dibromo-1-alkene 7 and a vinylstannane in a highly dipolar solvent capable of promoting HBr elimination to give internal alkynes.     

Theoretical studies of inclusion complexes of β-cyclodextrin with methylated benzoic acids

AM1 semiempirical molecular orbital calculations have been performed on the inclusion complexes of β-cyclodextrin (β-CD) with methylated benzoic acids in two orientations, the “head-first” and “tail-first” positions. In the former, the CO₂H group points toward the primary hydroxyls of the CD. In the latter, it points away from them. Out of 30 possible inclusion complexes, AM1 results predict only three clearly stable inclusion complexes. These are β-CD with 4-methyl benzoic acid in the head-first position, β-CD with 2,4-dimethyl benzoic acid in the head-first position, and β-CD with 3,5-dimethyl benzoic acid in the tail-first position. The orientations of the stable inclusion complexes correlate with the total number of intramolecular hydrogen bonds and intermolecular hydrogen bonds. The stability of a complex also correlates with the closeness of the host and guest geometries in the complex to their isolated molecule geometries. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 64 : 711–719, 1997     

阴离子插层镁铝水滑石结构及相互作用的理论研究

采用密度泛函理论(DFT)计算了MgAl-LDHs层板与无机阴离子(F^-、Cl^-、NO₃^-、CO₃^2-、SO₄^2-)和有机阴离子(水杨酸根离子([HO(C₆H₄)COO]^-)、苯甲酸根离子([(C₆H₅)COO]^-)、对二甲氨基苯甲酸根离子([p-(CH₃)₂N(C₆H₄)COO]^-)、十二烷基磺酸根离子[C₁₂H₂₅SO₃]^-、己烷基磺酸根离子[C₆H₁₃SO₃]^-、丙烷基磺酸根离子[C₃H₇SO₃]^-)间的相互作用,获得稳定超分子几何结构及相互作用能。层板主体与客体间存在较强的超分子作用,包括主客体间静电作用和氢键等。主、客体间相互作用能数值大小顺序为CO₃^2- > SO₄^2- > F^-> Cl^-> NO₃^-;[p-(CH₃)₂N(C₆H₄)COO]^-> [(C₆H₅)COO]^-> [HO(C₆H₄)COO]^-和[C₁₂H₂₅SO₃]^-> [C₆H₁₃SO₃]^- > [C₃H₇SO₃]^-。另外,还采用自然键轨道(NBO)计算和分析了LDHs 层板与阴离子间作用机理,从二阶微扰理论计算得到的稳定化能变化趋势与相互作用能数据基本吻合。     

Disinfection of seeds and sprout inhibition of potatoes with low energy electrons

Electrons at acceleration voltages of 170–190 kV reduced microbial count of seeds of adzuki bean, pot herb mustered and black gram to undetectable levels without any detrimental effects on the germination ability. However, electrons at 200 kV or higher affected the growing of black gram sprouts. The energies of electrons at the surface of seed (15 cm distance from the accelerator’s window) at acceleration voltages of 170–190 kV were estimated to be 60–90 kV, based on the stopping powers of titanium and air. Electrons at acceleration voltages of 250 kV or higher inhibited sprouting of potato tubers of various cultivars. The results suggest the efficacy of low energy electron treatment for disinfection of seeds and sprout inhibition of potatoes.     

Gas chromatographic optimization studies on the side chain and ring regioisomers of methylenedioxymethamphetamine

Gas chromatographic (GC) optimization studies are conducted for the 10 methylenedioxyphenethylamine regioisomeric substances related to the drug of abuse 3,4-methylenedioxymethamphetamine (MDMA, Ecstasy). These 10 compounds, having the same molecular weight and equivalent major mass spectral fragments, are not completely resolved using typical GC-mass spectrometry screening methods for illicit drugs. MDMA coelutes with at least one nondrug regioisomer under standard drug screening conditions. Separation of the 10 regioisomers is studied using stationary phases of varying polarities. Resolution optimization shows that very slow program rates give the best separation for the nonpolar stationary phases, requiring analysis times of as much as 85 min. Narrow-bore columns containing the same nonpolar stationary phases improve the analysis time to approximately 29 min. The polar stationary phase DB-35MS allows high-temperature programming rates, yielding complete resolution of all 10 compounds in less than 7 min. Temperature program optimization studies on the DB-35MS phase allow the separation time to be reduced to approximately 4.5 min.     

A preference for edgewise interactions between aromatic rings and carboxylate anions: the biological relevance of anion-quadrupole interactions

Noncovalent interactions are quite important in biological structure-function relationships. To study the pairwise interaction of aromatic amino acids (phenylalanine, tyrosine, tryptophan) with anionic amino acids (aspartic and glutamic acids), small molecule mimics (benzene, phenol or indole interacting with formate) were used at the MP2 level of theory. The overall energy associated with an anion-quadrupole interaction is substantial (-9.5 kcal/mol for a benzene-formate planar dimer at van der Waals contact distance), indicating the electropositive ring edge of an aromatic group can interact with an anion. Deconvolution of the long-range coplanar interaction energy into fractional contributions from charge-quadrupole interactions, higher-order electrostatic interactions, and polarization terms was achieved. The charge-quadrupole term contributes between 30 to 45% of the total MP2 benzene-formate interaction; most of the rest of the interaction arises from polarization contributions. Additional studies of the Protein Data Bank (PDB Select) show that nearly planar aromatic-anionic amino acid pairs occur more often than expected from a random angular distribution, while axial aromatic-anionic pairs occur less often than expected; this demonstrates the biological relevance of the anion-quadrupole interaction. While water may mitigate the strength of these interactions, they may be numerous in a typical protein structure, so their cumulative effect could be substantial.     

Theoretical studies on pyridoxal 5'-phosphate-dependent transamination of alpha-amino acids

Density functional methods have been applied to investigate the irreversible transamination between glyoxylic acid and pyridoxamine analog and the catalytic mechanism for the critical [1,3] proton transfer step in aspartate aminotransferase (AATase). The results indicate that the catalytic effect of pyridoxal 5'-phosphate (PLP) may be attributed to its ability to stabilize related transition states through structural resonance. Additionally, the PLP hydroxyl group and the carboxylic group of the amino acid can shuttle proton, thereby lowering the barrier. The rate-limiting step is the tautomeric conversion of the aldimine to ketimine by [1,3] proton transfer, with a barrier of 36.3 kcal/mol in water solvent. A quantum chemical model consisting 142 atoms was constructed based on the crystal structure of the native AATase complex with the product L-glutamate. The electron-withdrawing stabilization by various residues, involving Arg386, Tyr225, Asp222, Asn194, and peptide backbone, enhances the carbon acidity of 4'-C of PLP and Calpha of amino acid. The calculations support the proposed proton transfer mechanism in which Lys258 acts as a base to shuttle a proton from the 4'-C of PLP to Calpha of amino acid. The first step (proton transfer from 4'-C to lysine) is shown to be the rate-limiting step. Furthermore, we provided an explanation for the reversibility and specificity of the transamination in AATase.     

Theoretical studies on electronic structure and magnetic properties of mixed‐valence uteroferrin active site

The electronic structure and magnetic interaction of the active site of pig purple acid phosphatase (PAP, uteroferrin) were investigated using pure DFT (UBLYP) and hybrid DFT methods (UB3LYP and UB2LYP). Uteroferrin catalyzes the hydrolysis of a phosphate ester under acidic conditions and contains a binuclear iron center. The mammalian PAPs are expected to be targets for drug design of osteoporosis. Their active sites are typical examples of the Fe(II)‐Fe(III) mixed‐valence system. We studied double exchange interaction of the mixed‐valence system, using the potential energy difference between the Fe(II)‐Fe(III) and the Fe(III)‐Fe(II) states. The pathway of the antiferromagnetic coupling between Fe(III) and Fe(II) were also discussed by using chemical indices, which are evaluated by the occupation numbers of singly occupied natural orbitals. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010