Electron and nuclear dynamics in many-electron atoms, molecules and chlorophyll-protein complexes: A review

It has been shown [V.A. Shuvalov, Quantum dynamics of electrons in many-electron atoms of biologically important compounds, Biochemistry (Mosc.) 68 (2003) 1333-1354; V.A. Shuvalov, Quantum dynamics of electrons in atoms of biologically important molecules, Uspekhi biologicheskoi khimii, (Pushchino) 44 (2004) 79-108] that the orbit angular momentum L of each electron in many-electron atoms is L = mVr = n? and similar to L for one-electron atom suggested by N. Bohr. It has been found that for an atom with N electrons the total electron energy equation E = −(Z^eff)²e⁴m/(2n²?²N) is more appropriate for energy calculation than standard quantum mechanical expressions. It means that the value of L of each electron is independent of the presence of other electrons in an atom and correlates well to the properties of virtual photons emitted by the nucleus and creating a trap for electrons. The energies for elements of the 1st up to the 5th rows and their ions (total amount 240) of Mendeleev' Periodical table were calculated consistent with the experimental data (deviations in average were 5 × 10^− 3). The obtained equations can be used for electron dynamics calculations in molecules. For H₂ and H₂⁺ the interference of electron-photon orbits between the atoms determines the distances between the nuclei which are in agreement with the experimental values. The formation of resonance electron-photon orbit in molecules with the conjugated bonds, including chlorophyll-like molecules, appears to form a resonance trap for an electron with E values close to experimental data. Two mechanisms were suggested for non-barrier primary charge separation in reaction centers (RCs) of photosynthetic bacteria and green plants by using the idea of electron-photon orbit interference between the two molecules. Both mechanisms are connected to formation of the exciplexes of chlorophyll-like molecules. The first one includes some nuclear motion before exciplex formation, the second one is related to the optical transition to a charge transfer state.     

A new look on the formation and interaction of elementary particles in atoms and molecules including photoreaction centers

Possible role of high-energy bosons (virtual photons) is discussed with respect to the formation of elementary particles and their interaction in nucleus, many-electron atom, and molecule including photoreaction centers. Using properties of the photons, the expressions for calculations of the mass of particles, of the energy of electrons and their distances from nucleus in atoms, of the dissociation energy and distances between atoms in molecules were found which give results in good agreement with experimental data. This approach allows doing calculations in rather complicated system like photoreaction centers in which chlorophyll molecules form electron transfer chain.     

Syntheses, crystal structures and antimicrobial activities of monomeric 8-coordinate, and dimeric and monomeric 7-coordinate bismuth(III) complexes with tridentate and pentadentate thiosemicarbazones and pentadentate semicarbazone ligands

Novel bismuth(III) complexes 1-4 with the tridentate thiosemicarbazone ligand of 2N1S donor atoms [Hmtsc (L1); 2-acetylpyridine (4N-morpholyl thiosemicarbazone)], the pentadentate double-armed thiosemicarbazone ligand of 3N2S donor atoms [H2dmtsc (L3); 2,6-diacetylpyridine bis(4N-morpholyl thiosemicarbazone)] and the pentadentate double-armed semicarbazone ligand of 3N2O donor atoms [H2dasc (L4b); 2,6-diacetylpyridine bis(semicarbazone)], were prepared by reactions of bismuth(III) nitrate or bismuth(III) chloride and characterized by elemental analysis, thermogravimetric and differential thermal analysis (TG/DTA), FTIR and NMR (1H and 13C) spectroscopy. The crystal and molecular structures of complexes 1, 2a, 2b and 4b, and the "free" ligand L1 were determined by single-crystal X-ray structure analysis. The dimeric 7-coordinate bismuth(III) complex [Bi(dmtsc)(NO3)]2, 1, and the monomeric 7-coordinate complexes [Bi(Hdasc)(H2O)](NO3)2.H2O (major product), 2a, and [Bi(dasc)(H2O)]NO3.H2O (minor product), 2b, all with pentagonal bipyramidal bismuth(III) centers, are depicted with one electron pair (6s2) of the bismuth(III) atom, deprotonated forms of multidentate thiosemicarbazone or semicarbazone ligands, and monodentate NO3 or H2O ligands, respectively. These complexes are related to the positional isomers of one electron pair of the bismuth(III) atom; 1 has an electron pair positioned in the pentagonal plane (basal position), while 2a and 2b have an electron pair in the apical position. The monomeric 8-coordinate complex [Bi(mtsc)2(NO3)], 4b, which was obtained by slow evaporation in MeOH of the 1.5 hydrates 4a, was depicted with one electron pair of the bismuth(III) atom, two deprotonated mtsc- ligand and one nitrate ion. On the other hand, crystals of the complex "[Bi(mtsc)Cl2]", 3, prepared by a reaction of BiCl3 with L1 showed several polymorphs (3a, 3b, 3c and 3d) due to coordination and/or solvation of dimethyl sulfoxide (DMSO) used in the crystallization. Bismuth(III) complexes 1 and 4a showed selective and effective antibacterial activities against Gram-positive bacteria. The structure-activity relationship was discussed.     

Contributions to quantum biology. I. Mobile electronic characteristics of riboflavin radicals

Quantum biology is the quantum mechanical study of electrons in molecules of biological interest. This requires the solution of problems involving many electrons. Approximation methods are therefore necessary and are discussed. The present study, concerned with the mobile electrons in riboflavin (FMN) and its radicals (FMN⁻, FMNH and FMNH₂ ⁺), is based on the approximation method, developed by B. Pullman and A. Pullman. The solution of the eigenvalue problems so obtained gives the energy levels of the mobile electron systems involved. The corresponding eigenvectors yield the mobile electronic charges of the atoms of riboflavin radicals which have contributed mobile electrons. Important differences of the net charge distributions of these radicals are emphasized. The longest wave length of light absorption is calculated from the obtained energy levels and agrees, within the accuracy of the method, with corresponding experimental results. From the appropriate calculated results, electronic assignments are obtained for the experimental transitions involved.     

Experimental and theoretical study of the near IR emission of xenon excited by a fast electron beam

Emission of xenon excited by a 120-keV electron beam at gas pressures of 100, 200, 500, and 760 Torr nm was studied experimentally and theoretically. More than 30 spectral lines were identified in the wavelength range of 750–1000 nm. A self-consistent kinetic model is developed to calculate the emission intensity of xenon atoms in the near IR range. The model includes balance equations for the number densities of electrons, ions and excimer molecules; equations for the populations of electron levels; and the Boltzmann equation for the low-energy part of the electron energy distribution function with a source of slow electrons. Excitation and ionization rates of xenon by the beam electrons and the energy spectrum of slow electrons are calculated by the Monte Carlo method. It is shown that, under these conditions, the main mechanism of xenon atom excitation is dissociative recombination of Xe₃ ⁺ ions.     

Hydration of transfer RNA molecules: a crystallographic study

Four crystal structures of transfer RNA molecules were refined at 3 A resolution with the inclusion of the solvent molecules found in the difference maps: yeast tRNA-phe in the orthorhombic form, yeast tRNA-phe in the monoclinic form and yeast tRNA-asp in the A and B forms. Over 100 solvent molecules were located in each tRNA crystal. Several hydration schemes are found repeatedly in the 4 crystals. The tertiary interactions in the corner of the L-shaped molecule attract numerous solvent molecules which bridge the ribose hydroxyl O(2') atoms, base exocyclic atoms and phosphate anionic oxygen atoms. Conservation of bases leads to conservative localized hydration patterns. Several solvent molecules are found stabilizing unusual base pairs like the G-U pairs and those involving the pseudouridine base. Water bridges between the O(2') and the exocyclic atom O2 of pyrimidines or the N3 atom of purines are common. Water bridges occur frequently between successive anionic oxygen atoms of each strand as well as between N7 or other exocyclic atoms of successive bases in the major groove. Magnesium ions or spermine molecules are found to bind in the major groove of tRNA helices without specific interactions.     

Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H₂O)_n (n = 1–3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H₂O)_n (n = 1–3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1–3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H₂O)₃ complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.     

13C, 15N, and 31P NMR studies on 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans

The interaction between the apoprotein of 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans and the prosthetic group FAD has been investigated by 13C, 15N, and 31P NMR techniques. The FAD prosthetic group was selectively enriched in 13C and 15N isotopes by adding isotopically labeled riboflavin derivatives to the growth medium of riboflavin-requiring mutant cells. In the oxidized state the chemical shift of the C(7) and C(8) atoms indicates that the xylene moiety of the isoalloxazine ring is embedded in a hydrophobic environment. The polarization of the isoalloxazine ring as a whole is, however, much more comparable to that of free flavin in a polar and protic environment than to free flavin in an apolar environment. The polarization of the ring system can be ascribed to strong hydrogen bonds between the apoprotein and the two carbonyl groups. The binding of the competitive inhibitor, 6-hydroxy-D-nicotine, influences the resonances of the C(4a) and the N(5) atoms strongly. It is suggested that these shifts are due to a strong hydrogen-bonding interaction between the N(5) atom and the inhibitor. On reduction all resonances, except those of the C(10a) and the N(1) atoms, shift upfield, indicating the increased electron density in the ring system. In the dithionite-reduced enzyme, the ring system is bent at the N(5) position. Due to the bending of the N(5) atom and the sp2 hybridized N(10) atom, electron density from the N(10) atom is reallocated at the C(4) carbonyl group. In contrast, in the substrate-reduced enzyme the N(5) atom is almost completely sp2 hybridized, yielding a rather planar isoalloxazine ring.(ABSTRACT TRUNCATED AT 250 WORDS)     

Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains

The electronic properties of amino acid side-chains are emerging as an important factor in the preference for secondary structure in proteins. These properties have not been fully characterized, nor has their role in the behavior of peptides been explored in any detail. The present studies sought to evaluate several possibilities: 1) that hydrophilicity can be expressed solely in electronic terms, 2) that substituent effects of side-chains extend across the peptide bond, and (3) nearest-neighbor effects in dipeptides correlate with secondary structural preferences. Quantum mechanics (QM) calculations were used to define the electronic properties of individual amino acids and dipeptides. It was found that the hydrophilicity of an amino acid side-chain can be accurately represented as a function of the electron densities of its component atoms. In addition, the nature of an amino acid in the second position of a dipeptide affects the electronic properties (Mulliken populations and electron densities) of the main-chain atoms of the first residue. Certain electronic features of the dipeptides strongly correlated with propensity for secondary structure. Specifically, Mulliken population data at the Calpha atom and N atom predicted preference for alpha-helices versus coil and strand conformations, respectively. Analysis of dipeptides arrayed in either helical or extended structures revealed lengthening of main-chain bonds in the alpha-helical conformations. A thorough characterization of the electronic properties of amino acids and short peptide segments may provide a better understanding of the forces that determine secondary structure in proteins.     

Role of secondary electrons and metastable atoms in the electron-beam activation of argon-silane mixtures

The energy and spatial degradation of the primary beam electrons and the production of high-energy secondary electrons in ionizing collisions are analyzed by solving the Boltzmann integral equation for the electron distribution function. The effect of the primary and secondary electrons on the direct ionization of an Ar-SiH₄ mixture, the production of metastable argon atoms, and the dissociation of monosilane molecules is investigated over a wide range of the beam electron energies, argon pressures, and monosilane concentrations. The influence of metastable Ar* atoms on the dissociation of SiH₄ is studied by using the balance equation for metastable argon atoms and the equation for the ambipolar diffusion of ions and low-energy secondary (plasma) electrons in the beam plasma. It is shown that the main contribution to the activation of an Ar-SiH₄ mixture in an electron-beam plasma is provided by secondary electrons with energies higher than the excitation threshold for argon and the dissociation threshold for monosilane, whereas the contribution from metastable argon atoms, though potentially being comparable with that from secondary electrons, is less than in gas-discharge plasmas.     

Synthesis, crystal structure and photoluminescent property of an iridium complex with coumarin derivative ligand

Novel iridium complex containing coumarin derivative as a cyclometalated ligand (L) and picolinate (pic) as the ancillary ligand, Ir(III)bis(3-(pyridin-2-yl)coumarinato N,C⁴)(picolinate) [Ir(L)₂(pic)], was synthesized and characterized. It was demonstrated that the iridium (III) ion in Ir(L)₂(pic) is hexacoordinated by two C atoms and two N atoms from 3-(pyridin-2-yl)coumarin ligands and one N atom and one O atom from picolinate ligand, displaying a distorted octahedral coordination geometry. The Ir(L)₂(pic) has very strong absorption and intensive emission at 532 nm. These results show the promising future of that Ir(L)₂(pic) in fabrication organic light-emitting diodes.     

Bis(2-methyltetrazole)dichlorocopper(II) is a layered coordination polymer built from dinuclear chloro-bridged Cu units linked by bridging tetrazoles. The first structurally and magnetically characterized complex of 2-monosubstituted tetrazoles

The data on synthesis, crystal structure, magnetic susceptibility and thermal properties of coordination compound of copper(II) chloride with 2-methyltetrazole (2mtet) of Cu(2mtet)₂Cl₂ composition are reported. The Cu atom environment forms an elongated octahedron, with two 2-methyltetrazole ligands (N4 bound) and two Cl atoms in the equatorial positions. Symmetry related 2-methyltetrazole ligand and Cl atom are in the axial positions. One of the two 2-methyltetrazole molecules of the asymmetric unit exhibits bridging properties being linked to two Cu atoms through two N atoms (i.e., N4 and N1) of the tetrazole ring, while the other ligand molecule is coordinated in monodentate fashion via one tetrazole N4 atom. The Cu-octahedra form dinuclear building bricks by sharing edges with equatorial and axial Cl atoms. These dinuclear units are linked together via bridging 2-methyltetrazole ligands to form infinite layers parallel to the plane. Magnetic properties of Cu(2mtet)₂Cl₂ and the data of quantum-chemical calculations of molecular electrostatic potential and energies of hydronation of nitrogen atoms for 2mtet using B3LYP/6-31G^* level of theory are in agreement with the structural data obtained.     

Synthesis, crystal structure, magnetic property and nuclease activity of a new binuclear cobalt(II) complex

One new binuclear Co(II) complex of N,N,N',N'-tetrakis(2-benzimidazolylmethyl)-2-hydroxyl-1,3-diaminopropane (HL), [Co(2)L(mu(2)-Cl)](ClO(4))(2) x 3CH(3)CN x C(2)H(5)OC(2)H(5) (1), has been synthesized and its crystal structure and magnetic properties are shown. In 1, each Co(II) atom has a distorted trigonal bipyramidal geometry with a N(3)OCl donor set. The central two Co(II) atoms are bridged by one alkoxo-O atom and one Cl atom with the Co1-Co2 separation of 3.239 A. Susceptibility data of 1 indicate strong intramolecular antiferromagnetic coupling of the high-spin Co(II) atoms. In this paper, the interaction with calf thymus DNA was investigated by UV absorption and fluorescent spectroscopy. Results show the complex binds to ct-DNA with a intercalative mode. The interaction between complex 1 and pBR322 DNA has also been investigated by submarine gel electrophoresis, noticeably, the complex exhibits effective DNA cleavage activity in the absence of any external agents.     

Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times

A system containing the globular protein azurin and 3,658 water molecules has been simulated to investigate the influence on water dynamics exerted by a protein surface. Evaluation of water mean residence time for elements having different secondary structure did not show any correlation. Identically, comparison of solvent residence time for atoms having different charge and polarity did not show any clear trend. The main factor influencing water residence time in proximity to a specific site was found to be its solvent accessibility. In detail for atoms belonging to lateral chains and having solvent-accessible surface lower than approximately 16 A(2)a relation is found for which charged and polar atoms are surrounded by water molecules characterized by residence times longer than the non polar ones. The involvement of the low accessible protein atom in an intraprotein hydrogen bond further modulates the length of the water residence time. On the other hand for surfaces having high solvent accessibility, all atoms, independently of their character, are surrounded by water molecules which rapidly exchange with the bulk solvent. Proteins 2000;39:56-67.     

Molecular Dynamics on an Excel Spreadsheet

Abstract

We discuss some of the problems that have frustrated the development of reliable model intermolecular potentials for polyatomic molecules. In particular, the usual assumption of an isotropic atom-atom model potential is analysed, and evidence for its inadequacies is presented. A new approach to designing model potentials, an anisotropic site—site model, is introduced by describing several applications to both small and organic molecules, including molecular dynamics and Monte Carlo simulations. The anisotropy required in an atom—atom potential can be directly linked to the non-spherical features in the valence electron distribution, such as lone pairs and π electrons. An accurate electrostatic model for these effects can be constructed from a distributed multipole analysis of the ab initio wavefunction. The empirically required forms of anisotropy in the repulsion potential can also be qualitatively linked to the molecular electron density difference map. Thus, consideration of the molecular bonding can be a useful indication of how to construct adequate model intermolecular pair potentials.     

Synthesis and structure-activity relationships of metal-ligand complexes that potently inhibit cell migration

We screened the National Cancer Institute Diversity Set compound collection for small molecules that affect mammalian cell migration and identified NSC 295642 as an inhibitor of cell motility with nanomolar potency. We found by LC-MS and X-ray crystallography that NSC 295642, a Cu(II) complex of the Schiff base product of condensation of S-benzyl dithiocarbazate and 2-acetylpyridine, has a bridged dimeric Cu2Cl2(L)2 structure with distorted square pyramidal geometry. Each of the two copper atoms is five-coordinated to one of the two tridentate chelating ligands and both bridging chlorine atoms. To define structure-activity relationships,we investigated the bioactivity of related metal-ligand complexes derived from different metal(II) atoms and different ligands. Complexation of the NSC 295642 ligand with Zn(II) or Ni(II), delivered as metal(II) chloride salts under conditions identical to those used for preparation of the original Cu(II) complex, instead results in distorted octahedral bis-chelate structures, where a single metal atom is six-coordinated to two ligands. The Zn(L)2 complex possesses a potency similar to that of the Cu2Cl2(L)2 complex, while the Ni(L)2 has no antimigratory activity at all. We carried out density functional theory calculations to obtain the electronic ground state geometry of the complexes, both in vacuum and implicit water solvent. The X-ray crystal and energy-minimized structures are very similar and exhibit a transoid orientation of the S-benzyl groups relative to the central metal-coordinated rings for both of the bioactive Cu2Cl2(L)2 and Zn(L)2 complexes, despite their different coordination geometries. In contrast, the biologically inactive Ni(L)2 complex adopts a cisoid conformation. Varying the ligand structure, we found that hydrophobic S-alkylaryl groups are required for activity. Complexes with a simple S-methyl group, S-benzyl groups with polar substitutions or a carboxylated pyridine ring exhibit dramatically reduced activity. We tested the most potent metal-ligand complex in a number of cancer cell lines and found cell-type selectivity in its effect on cell motility. Collectively, these results suggest that a two-ligand structure with bulky nonpolar S-substituents in a transoid conformation is important for the antimigratory activity of these metal-ligand complexes.     

Multi-isomorphous replacement phasing of the earthworm fibrinolytic enzyme component A from Eisenia fetida

Thrombosis is one of the most widely occurring diseases in modern life, which often causes disability and death. Fibrinolytic enzymes degrade fibrin, the major protein component of blood clots, and eventually lead to thrombolysis. Medications using fibrinolytic enzymes are the most effective methods used in the treatment of thrombosis. A variety of fibrinolytic enzymes, such as tPA, uPA, and streptokinase, have been extensively studied and used as thrombolytic agents in clinic. However, thes…     

Orientation of chromophores in reaction centers of Rhodopseudomonas sphaeroides: a photoselection study.

The relative orientation of the pigments of reaction centers from Rhodopseudomonas sphaeroides has been studied by the photoselection technique. A high value (+0.45) of p=(delta AV--delta AH)/(delta AV + delta AH) is obtained when exciting and observing within the 870 nm band which is contradictory to the results of Mar and Gingras (Mar, T. and Gringras, G. (1976) Biochim. Biophys. Acta 440, 609-621) and Shuvalov et al. (Shuvalov, V.A., Asadov, A.A. and Krakhmaleva, I.N. (1977) FEBS Lett. 16, 240-245). It is shown that the low values of p obtained by both groups were erroneous due to excitation conditions. Analysis of the polarization of light-induced changes when exciting with polarized light in single transitions (spheroiden band and bacteriopheophytin Qx bands) enable us to propose a possible arrangement of the pigments within the reaction center. It is concluded that the 870 nm band corresponds to a single transition and is one of the two bands of the primary electron donor (P-870). The second band of the bacteriochlorophyll dimer is centered at 805 nm. The Qx transitions of the molecules constituting the bacteriochlorophyll dimer are nearly parallel (angle less than 25 degrees). The two bacteriopheophytin molecules present slightly different absorption spectra in the near infra-red. Both bacteriopheophytin absorption bands are subject to a small shift under illumination. The angle between the Qy bacteriopheophytin transitions is 55 degrees or 125 degrees. Both Qy transitions are nearly perpendicular to the 870 nm absorption band. Finally, the carotenoid molecules makes an angle greater than 70 degrees with the 870 nm band and the other bacteriochlorophyll molecules.     

Synthesis,crystal structure,antitumor activity and DNA-binding study on the Mn(II) complex of 2H-5-hydroxy-1,2,5-oxadiazo[3,4-f]1,10-phenanthroline

The complex [Mn(L)(NO₃)₂(H₂O)₂] (1) (L=2H-5-hydroxy-1,2,5-oxadiazo[3,4-f]1,10-phenanthroline) was synthesized and characterized by elemental analysis, IR and UV. The crystal and molecular structure of 1 was determined by single-crystal X-ray diffraction; crystal data: light yellow, monoclinic, space group P2₁/n, Z=4, a=7.432(2) Å, b=9.582(3) Å, c=23.445(7) Å, β=90.519(5)°. The Mn atom in 1 is hexa-coordinated in a distorted octahedral arrangement by two N atoms of the ligand L and four O atoms of two water molecules and two nitrate anions. Biological tests in vitro showed that 1 has significant antitumor activity against HL-60, KB, Hela and BGC-823 cells. The interaction of 1 with calf thymus DNA was investigated by absorption titration, thermal denaturation and viscosity measurements. The results suggest that 1 binds with DNA by intercalating via the ligand L.     

Circular dichroism of surface complexes based on quantum dots and azo dye

Chiral properties of surface complexes based on CdSe/ZnS quantum dots (QDs) and 1‐(2‐pyridylazo)‐2‐naphthol (PAN) azo dye were investigated by circular dichroism spectroscopy. The use of L‐, D‐cysteine (Lcys, Dcys) capping ligands allowed us to obtain water‐soluble chiral QD‐PAN complexes. The characterization of the complexes was performed by UV‐vis, FTIR, and CD spectroscopy. Quantum chemical TDDFT calculated CD spectra reproduced the experimentally observed sign patterns, which originate from binding Lcys or Dcys and PAN molecules to the same Zn atom on the QD surface. The resulting complex is characterized by a large circular dichroism in comparison with an ordinary QD chirality induced by cysteine molecules. The pattern of CD signal is the same for Lcys and Dcys ligands in chiral QD‐PAN complex.