Electron donor-acceptor complexes: Evaluation of MNDO as a computational tool to probe intermolecular interactions

Donor-acceptor pairs form EDA complexes that exist as conformational isomers exhibiting different ground-state and photochemical properties. We have sought a rapid, general, and accurate quantum mechanical computational method to generate potential energy surfaces that are representative of the donor-acceptor intermolecular interactions at the self-consistent field (SCF) level. The semiempirical molecular orbital (MO) method MNDO has been compared to ab initio methods to assess its behavior with respect to energy, dipole moment and ionization potential shifts. MNDO correctly distinguishes between repulsive and bound EDA complex states at the SCF level and produces potential curves that are smooth and free of spurious minima or cusps. MNDO curves are systematically more repulsive than those for ab initio STO-3G calculations; calculated interaction energies exhibit a mean absolute deviation of 2.90 kcal/mol. MNDO appears to provide a reliable qualitative estimate of the nondispersion portion of the interaction energy. Limitations and errors arising from minimal basis sets, single determinants, and neglect of dispersion are discussed.     

Gels from a semifluorinated n-alkane in fluorinated solvents as a probe for intermolecular interactions

Diblock semifluorinated n-alkanes can form aggregates and gels in fluorinated solvents. We have investigated the thermal behavior of binary mixtures comprising F(CF₂)₈(CH₂)₁₆H and fluorinated solvents. The solvents were perfluorohexane, perfluoroheptane, perfluorooctane, perfluorooctyl bromide, perfluorodecalin, and perfluorotributylamine. The phase diagrams were used to calculate the activity coefficients of the two components and the main excess thermodynamic functions. The solubility and self-assembly behavior of F₈H₁₆ in the fluorinated solvents are related to the different solute–solvent dispersion interactions that depend on the polarizabilities and ionization potentials of the interacting species, and on the structural properties of the solvent.     

Energy screening for the incremental scheme: application to intermolecular interactions

A systematic screening procedure for small contributions in the incremental expansion of the correlation energy is presented. The performance of the proposed scheme is checked for the calculation of intermolecular interactions in realistic test systems as large as a guanine-cytosine base pair. It is found that the computational cost for the incremental expansion can be reduced considerably without significant loss of accuracy. Typically, the errors of the systems investigated here amount to <3.4, 0.22, and 0.06% for second-, third-, and fourth-order expansions, respectively. For almost all cases, the error in the total correlation energy can be kept below 1 kcal/mol with respect to the canonical CCSD result if the incremental series is truncated in a proper way.     

Variable-temperature fourier transform IR as a probe of intermolecular forces: Application to organotin compounds

The medium and strong IR absorptions of a number of organometallic complexes of Sn(IV) have been studied as a function of temperature over the range 78     

Capillary electrophoresis as a probe of enantiospecific interactions between photoactive transition metal complexes and DNA

Recently, we have demonstrated the capacity to separate chiral transition metal (TM) complexes of the type [M(diimine)(3)](n+) using CE buffers containing chiral tartrate salts. In separate work, several chromium(III)-tris-diimine complexes in particular have been shown to bind enantioselectively with calf-thymus (CT) DNA, and a qualitative assessment of the relative strength and enantiospecificity of this interaction is of significant interest in the characterization of these complexes as potential DNA photocleavage agents. Here, we describe two convenient approaches to investigate such binding behavior using chiral CE. For complexes with lower DNA affinities exhibiting primarily surface binding, DNA itself is used as the chiral resolving agent in the electrophoretic buffer. In this approach, resolution of the TM complexes into their Lambda and Delta isomers is achieved with the isomer eluting later exhibiting superior binding affinity toward DNA. For more strongly bound TM complexes containing ligands known to intercalate with DNA, the [Cr(diimine)(3)](3+) complexes are preincubated with oligonucleotide and subsequently enantiomerically resolved in a dibenzoyl-L-tartrate buffer system that facilitates analysis of the unbound TM species only. Differences in isomer binding affinity are distinguished by the relative peak areas of the Lambda- and Delta-isomers, and relative binding strengths of different complexes can be inferred from comparison of the total amount of unbound complex at equivalent DNA/TM ratios.     

Observation of intermolecular interactions in large protein complexes by 2D-double difference nuclear Overhauser enhancement spectroscopy: application to the 44 kDa interferon-receptor complex

NMR detection of intermolecular interactions between protons in large protein complexes is very challenging because it is difficult to distinguish between weak NOEs from intermolecular interactions and the much larger number of strong intramolecular NOEs. This challenging task is exacerbated by the decrease in signal-to-noise ratio in the often used isotope-edited and isotope-filtered experiments as a result of enhanced T(2) relaxation. Here, we calculate a double difference spectrum that shows exclusively intermolecular NOEs and manifests the good signal-to-noise ratio in 2D homonuclear NOESY spectra even for large proteins. The method is straightforward and results in a complete picture of all intermolecular interactions involving non exchangeable protons. Ninety-seven such (1)H-(1)H NOEs were assigned for the 44 KDa interferon-α2/IFNAR2 complex and used for docking these two proteins. The symmetry of the difference spectrum, its superb resolution, and unprecedented signal-to-noise ratio in this large protein/receptor complex suggest that this method is generally applicable to study large biopolymeric complexes.     

甲基氟苯-氩复合物的分子间振动

在超声分子束装置上,利用多光子共振光电离和飞行时间质谱技术,观测到了三种甲基氟苯-氩复合物S1←S0电子态跃迁的两光子共振电离光谱。通过对光谱的分析和理论计算,获得了三种复合物内部分子音质伸缩振动和弯曲振动的频率。结果显示,F原子和CH3在苯环上取代H原子后,它们的相对位置对伸缩振影响很小,而与弯曲振动有较大的相关。另外,在复合物内部,Ar原子对甲基氟苯中的CH3内转动有明显的阻碍作用。     

The intermolecular interactions in the aminonitromethylbenzenes

The intermolecular non-covalent interactions in aminonitromethylbenzenes namely 2-methyl-4-nitroaniline, 4-methyl-3-nitroaniline, 2-methyl-6-nitroaniline, 4-amino-2,6-dinitrotoluene, 2-methyl-5-nitroaniline, 4-methyl-2-nitroaniline, 2,3-dimethyl-6-nitroaniline, 4,5-dimethyl-2-nitroaniline and 2-methyl-3,5-dinitroaniline were studied by quantum mechanical calculations at RHF/311++G(3df,2p) and B3LYP/311++G(3df,2p) level of theory. The calculations prove that solely geometrical study of hydrogen bonding can be very misleading because not all short distances (classified as hydrogen bonds on the basis of interaction geometry) are bonding in character. For studied compounds interaction energy ranges from 0.23 kcal mol⁻¹ to 5.59 kcal mol⁻¹. The creation of intermolecular hydrogen bonds leads to charge redistribution in donors and acceptors. The Natural Bonding Orbitals analysis shows that hydrogen bonds are created by transfer of electron density from the lone pair orbitals of the H-bond acceptor to the antibonding molecular orbitals of the H-bond donor and Rydberg orbitals of the hydrogen atom. The stacking interactions are the interactions of delocalized molecular π-orbitals of the one molecule with delocalized antibonding molecular π-orbitals and the antibonding molecular σ-orbital created between the carbon atoms of the second aromatic ring and vice versa.      

Single molecule spectroscopy as a probe for dye-polymer interactions

Experimental (Single Molecule Spectroscopy) and theoretical (quantum-chemical calculations and Monte Carlo and molecular dynamics simulations) techniques are combined to investigate the behavior and dynamics of a polymer-dye molecule system. It is shown that the dye molecule of interest (1,1'-dioctadecyl-3,3,3',3'-tetramethylindo-dicarbocyanine) adopts two classes of conformations, namely planar and nonplanar ones, when embedded in a poly(styrene) matrix. From an in-depth analysis of the fluorescence lifetime trajectories, the planar conformers can be further classified according to the way their alkyl side chains interact with the surrounding poly(styrene) chains.     

Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions

Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11.     

Substrate-mediated intermolecular interactions: a quantitative single molecule analysis

Long-range intermolecular interactions mediated by the surface are believed to be responsible for many effects in surface science, including molecular ordering, formation of nanostructures, and aligning reactive intermediates in catalysis. Here, we use scanning tunneling microscopy to probe the weak substrate-mediated interactions in benzene overlayers on Au{111} at 4 K. Using an automated procedure to monitor single molecule motion, we are able to quantify the substrate-mediated interaction strength. We explain quantitatively both the kinetics of the benzene motion and the thermodynamics that determine the packing structures benzene adopts in this system in light of these substrate-mediated interactions.     

Evidence for the preservation of specific intermolecular interactions in gaseous protein-oligosaccharide complexes

Arrhenius parameters, obtained with the blackbody infrared radiative dissociation technique, are reported for the dissociation of a series of gaseous protonated complexes composed of mutants of a single chain variable fragment (scFv) of the monoclonal antibody Se155-4 and three trisaccharide ligands. Hydrogen bonding between a ligand and a particular amino acid residue is identified from a comparison of activation energies measured for the complex of the unmodified scFv and the corresponding mutant. It is shown that the specific hydrogen bond between His(101H) and Man C-4 OH is preserved in the gaseous complex.     

Real-time dipole orientational imaging as a probe of ligand-protein interactions

Single-molecule orientational imaging using total internal reflection fluorescence microscopy has been employed to investigate the dynamics of a protein-ligand system. Emission patterns from single tetramethylrhodamine (TMR)-biocytin molecules bound to streptavidin show that the TMR dipole adopts a limited number of favored orientations. The angular trajectories of individual dipoles exhibit remarkably similar patterns that are characteristic of single TMR molecules interacting with a relatively homogeneous population of nanoenvironments. Analysis of the polar and azimuthal angle distributions reveals a tendency for the dipole to assume three primary and two secondary orientations. Autocorrelation analysis of the dipole trajectories shows a predominantly bimodal behavior in the reorientation rates with the slow and fast components corresponding to the primary and secondary orientations, respectively. A number of mechanisms by which the observed orientations might be stabilized have been considered, in particular specific interactions between the zwitterionic TMR probe and charged residues on the streptavidin surface. Variations in the reorientation rates have been discussed in terms of local thermal fluctuations in the protein.     

AXAFS as a probe of charge redistribution within organometallic complexes

Atomic XAFS on [PtCl(NCN)-Z] pincer complexes shows it to be a sensitive probe for the determination of the electron density on the metal atom, similar yet complementary to NMR.     

Structure and intermolecular interactions in complexes with hydrogen bond of a series of bifunctional nitrogen-containing compounds

By means of IR absorption spectra, low temperature ¹H and ¹⁵N NMR spectra, and quantum chemical calculations we study the structure of complexes with hydrogen bond of molecular and ionic character formed by nitrogen-containing compounds able to be both proton donors and acceptors simultaneously and the interaction specificity in them. Spectroscopic, steric, and thermodynamic characteristics of diphenyltriazene, 3,5-dimethylpyrazole, and diphenylformamidine homoassociates and heterocomplexes of these compounds with carboxylic acids and various proton donating molecules are obtained. Quantum chemical calculations of the structure of complexes and vibrational frequencies in IR spectra are made in the harmonic approximation and with regard to anharmonicity corrections. Calculations taking into account anharmonicity of vibrations are shown to produce the results closest to the experimental data.     

ESR studies on the intermolecular interactions of the mononitrosyl chelate complexes of iron

Using ESR the exchange of ligands was studied between mononitrosyl chelate complexes of iron and chelate complexes of nickel with the following ligands: dithiocarbamate (dtc), dithiophosphate (dtp), dithiocarbonate (xant), 8-quinolinethiolate, 8-hydroxyquinoline, acetylacetonate and o-hydroxy- benzylideneaniline. For some mixed-ligand complexes the exchange of the covalency of the metal—ligand bond was evaluated. The interaction of the mononitrosyl complexes with Lewis acids (I₂ and Br₂) and bases (pyridine, DMFA and DMSO) was studied in the cases of Fe(NO)(dtc)₂, Fe(NO)(dtp)₂ and Fe(NO)(xant)₂. In both of the latter cases the interactions with Lewis acids and bases led to the formation of paramagnetic dinitrosyl complexes, while with Fe(NO)(dtc)₂ hexacoordinated mononitrosyl complexes were formed. A reaction pathway is suggested and discussed for the formation of the dinitrosyl complexes and their composition.     

The chlorine isotope effect as a vibrational probe to conformational and intermolecular effects in liquid C6H5CCl3

The concentration-dependent isotopic resolved structure of the 409 cm⁻¹ Raman band of C₆H₅CCl₃ prompts a vibrational spectra study of this compound. The gathering of spectroscopic vibrational data suggests the existence of two important effects, the intramolecular conformational effects and the intermolecular interactions. In particular, it is concluded that the occurrence of two symmetrical conformations whose relative abundance is dependent on the concentration of the sample can well interpret the peculiar features exhibited by the CCl₃ stretching band at ca. 409 cm⁻¹.