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.     

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.     

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.     

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.     

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.     

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.     

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.

     

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     

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.     

Theoretical studies on the potential energy surfaces and vibrational energy levels of HXeF and HXeCl

The potential energy surfaces for the electronic ground state of the HXeCl and HXeF molecules areconstructed by using the internally contracted multi-reference configuration interaction with theDavidson correction(icMRCI Q)method and large basis sets.The stabilities and dissociation barriersare identified from the potential energy surfaces.The three-body dissociation channel is found to bethe dominate dissociation channel for HXeCl,while two dissociation channels are possible and com-petitive for HXeF.Based on the obtained potentials,vibrational energy levels of HXeCl and HXeF arecalculated using the Lanczos algorithm.Our theoretical results are in good agreement with the avail-able observed values.Particularly,the calculated fundamental frequency of the H—Xe stretching vi-bration including the Xe matrix effect of HXeCl is found to be 1666.6 cm-1,which is only 17.6 cm-1higher than the recently observed value of 1649 cm-1.     

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.     

Metal-sulfur valence orbital interaction energies in metal-dithiolene complexes: determination of charge and overlap interaction energies by comparison of core and valence ionization energy shifts

The electronic interactions between metals and dithiolenes are important in the biological processes of many metalloenzymes as well as in diverse chemical and material applications. Of special note is the ability of the dithiolene ligand to support metal centers in multiple coordination environments and oxidation states. To better understand the nature of metal-dithiolene electronic interactions, new capabilities in gas-phase core photoelectron spectroscopy for molecules with high sublimation temperatures have been developed and applied to a series of molecules of the type Cp(2)M(bdt) (Cp = η(5)-cyclopentadienyl, M = Ti, V, Mo, and bdt = benzenedithiolato). Comparison of the gas-phase core and valence ionization energy shifts provides a unique quantitative energy measure of valence orbital overlap interactions between the metal and the sulfur orbitals that is separated from the effects of charge redistribution. The results explain the large amount of sulfur character in the redox-active orbitals and the 'leveling' of oxidation state energies in metal-dithiolene systems. The experimentally determined orbital interaction energies reveal a previously unidentified overlap interaction of the predominantly sulfur HOMO of the bdt ligand with filled π orbitals of the Cp ligands, suggesting that direct dithiolene interactions with other ligands bound to the metal could be significant for other metal-dithiolene systems in chemistry and biology.     

Influence of the side chain on the stability of Schiff-bases formed between pyridoxal 5′-phosphate and amino acids

The stability of some Schiff-bases formed between PLP and different amino acids has been investigated in a wide range of pH. The kinetic constants of formation of these compounds and their hydrolysis rate constants have been determined. Results show that the α-position of the carboxyl group of amino acid plays an important role on the mechanism of water attack upon the C?N? bond. The absence of ionic groups in the surroundings of that bond must be an important factor of stability. Bulky hydrophobic substituents in the amino acid, near the amine part, protect the imine bond against hydrolysis.     

Theoretical studies on the protonation behavior of tropone and its metal complexes

Density functional theory calculations were carried out to investigate structures and stabilities of tropone and troponeiron complexes, (tropone)Fe(CO)₃, (tropone)Fe(CO)₂(PH₃) and (tropone)Fe(PH₃)₃, and their protonated species. The results show that the oxygen-protonated tropone is more stable than the carbon-protonated tropone. On the contrary, in the troponeiron complexes, the carbon protonated species are more stable than the oxygen protonated species. In the neutral and oxygen-protonated complexes, the tropone and oxygen-protonated tropone ligands are η⁴-coordinated. In the carbon-protonated complexes, the carbon-protonated tropone ligand is η⁵-coordinated. The results also show that the metal shift for complexes containing phosphine ligands is more difficult than that for those containing carbonyl ligands. For the neutral methyl-substituted troponeiron complexes, steric effect was found to play a key role in determining the relative stability of the regioisomers. For their protonated species, the electron-donating properties of the methyl substituent(s) were found to be important in determining the relative stability among the different regioiosmers.     

Theoretical studies on the topographical features and energetics of diacetylene-hydrogen fluoride complexes

Ab initio supermolecular SCF calculations have been carried out on diacetylene-HF complexes at the STO-4-31G level. The reverse σ (Rσ) complex has been found to have the lowest energy. Of the two π complexes. T and L, the symmetrical one T is found to be energetically less stable than the asymmetrical one L. Theoretical vibrational analysis tends to support this stability order. Electrostatic interaction energy calculations also lead to an almost identical sequence. Hydrogen bond energies corrected for basis set superposition error indicate that ΔE_H (Rσ) > ΔE_H (Tπ) ≈ ΔE_H (Lπ).     

Structural models of protein-DNA complexes based on interface prediction and docking

Protein-DNA interactions are the physical basis of gene expression and DNA modification. Structural models that reveal these interactions are essential for their understanding. As only a limited number of structures for protein-DNA complexes have been determined by experimental methods, computation methods provide a potential way to fill the need. We have developed the DISPLAR method to predict DNA binding sites on proteins. Predicted binding sites have been used to assist the building of structural models by docking, either by guiding the docking or by selecting near-native candidates from the docked poses. Here we applied the DISPLAR method to predict the DNA binding sites for 20 DNA-binding proteins, which have had their DNA binding sites characterized by NMR chemical shift perturbation. For two of these proteins, the structures of their complexes with DNA have also been determined. With the help of the DISPLAR predictions, we built structural models for these two complexes. Evaluations of both the DNA binding sites for 20 proteins and the structural models of the two protein-DNA complexes against experimental results demonstrate the significant promise of our model-building approach.     

Reactions in clusters of acetone and fluorinated acetones triggered by low energy electrons

Electron attachment to clusters of acetone (A), trifluoroacetone (TFA) and hexafluoroacetone (HFA) is studied in a crossed beam experiment with mass spectrometric detection of the anionic products. We find that the electron attachment properties in A change dramatically on going from isolated molecules to clusters. While single acetone is a very weak electron scavenger (via a dissociative electron attachment (DEA) resonance near 8.5 eV), clusters of A capture electrons at very low energy (close to 0 eV). The final ionic products consist of an ensemble of molecules (M) subjected to the loss of two neutral H₂ molecules ((M_n−2H₂)⁻, n ≥ 2). Their formation at low energies can only be explained by invoking new cyclic structures and polymers. In clusters of TFA, anionic complexes containing non-decomposed molecules (M_n⁻) including the monomer (M⁻) and ionic products formed by the loss of one and two HF molecules are observed. Loss of HF units is also interpreted by the formation of new cyclic structures in the anionic system. HFA is a comparatively stronger electron scavenger forming a non-decomposed anion via a narrow resonant feature near 0 eV in the gas phase. In HFA clusters, the non-decomposed parent anion is additionally observed at higher electron energies in the range 3–9 eV. The M⁻ signal carries signatures of self-scavenging processes, i.e., inelastic scattering by one molecule and capture of the completely slowed down electron by a second molecule within the same cluster. The scavenging spectrum is hence an image of the electronically excited states of the neutral molecule.     

Theoretical studies for Lewis acid-base interactions and C-H...O weak hydrogen bonding in various CO2 complexes

Comprehension of the basic concepts for the design of CO2-philic molecules is important due to the possibility for "green" chemistry in supercritical CO2 of substitute solvent systems. Lewis acid-base interactions and C-H...O weak hydrogen bonding were suggested as two key factors in the solubility of CO2-philic molecules. To isolate the stabilization energy of weak hydrogen bonding from the overall binding energy, high-level quantum mechanical calculations were performed for the van der Waals complexes of CO2 with methane, methylacetate, dimethylether, acetaldehyde, and 1,2-dimethoxyethane. Structures and energies were calculated at the MP2 level of theory using the 6-31+G(d) and aug-cc-pVDZ basis sets with basis set superposition error corrections. In addition, the single-point energies were calculated using recently developed multilevel methods. This study shows that the Lewis acid-base interaction has a significant impact on the complex stability compared to the C-H...O weak hydrogen bond. The additional stabilization energy of the cooperative weak hydrogen bond with alpha-proton of the carbonyl group was negligible on the enhancement of supercritical CO2 solubility. However, the stabilization energy was larger for the ether group, such that it may have an important role in increasing the supercritical CO2 solubility. Additional formation of cooperative weak hydrogen bonds may not further increase the solubility due to the stability reduction by steric hindrance.