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At least 1,063 records · Page 59Linked to original sources
PubMed1992

Protein: nucleic acid interactions. I. Electronic structures of cytosine, indole, and guanine complexes.

Low singlet transition energies and line strengths were calculated for the cytosine:indole:guanine complex by the INDO/1S-CI method. The chromophores were arranged in three sets of 270 intercalating geometries. Calculations were executed in the supermolecule model with single excited configurations. Errors due to basis set extension and incomplete configuration representation were assessed, for all chromophore pairs, by full BSSE correction calculations and inclusion of double-excited configurations. The intercalation-induced perturbations of the principal transitions are characterized by but not limited to (a) a decrease in strength of [pi*,pi] transitions, (b) increase in strength in [pi*,n] transitions, (c) splitting of [pi*,pi] transitions into components of unequal strength, and (d) energy and strength dependence in mixed transitions on rise and shift movements of the nucleic acid bases. These predictions are in accord with absorption, fluorescence emission, and scattering, and resonance Raman spectroscopic data on oligonucleotides and analogous aromatic complexes. The calculations suggest that major differences in intercalating coordinations are discernible in the near-uv spectroscopic domain of proteins and nucleic acids.

Cytosine↗
PubMed2003

On the electronic structures of the 1,3-diboracyclobutane-1,3-diyls and their valence isomers with a B2E2 skeleton (E=N, P, As).

The concept of through-space versus through-bond interactions on the stabilization of biradical structures with a singlet or triplet ground state is evaluated for the 1,3-diboracyclobutane-1,3-diyls and related congeners. Singlet biradicals are favored when the intermediate units E feature singlet character (PH(2) (+), AsH(2) (+)), while E fragments with triplet character (NH(2) (+)) induce small energy separations between the lowest singlet and triplet states. These considerations are supported by quantum chemical calculations with energy optimization at 1) MCSCF level plus MR-MP2 correction, 2) MR-MP2 level, and 3) two different types of density functional levels for the planar (D(2h)) geometries. The singlet-triplet energy separations in the planar compounds increase with increasing singlet stability of the corresponding E fragments. In addition to this newly developed principal features for singlet stabilization, which primarily occurs in bonded structures with higher main-group elements, the corresponding valence isomers with bicyclobutane, cyclobutene and cis-butadiene structures are investigated.

Journal Article↗
PubMed2003

Coordinated and clathrated guests in the 3infinity[Hg6As4]4+ bicompartmental framework: synthesis, crystal and electronic structure, and properties of the novel supramolecular complexes [Hg6As4](CrBr6)Br and [Hg6As4](FeBr6)Hg0.6.

Two new supramolecular complexes [Hg(6)As(4)](CrBr(6))Br (1) and [Hg(6)As(4)](FeBr(6))Hg(0.6) (2) have been prepared by the standard ampoule technique and their crystal structures determined. Both crystallize in the cubic space group Pa$\bar 3$ with the unit cell parameter a=12.275(1) (1) and 12.332(1) A (2), and Z=4. Their structures consist of bicompartmental, three-dimensional [Hg(6)As(4)](4+) frameworks with cavities of two different sizes occupied by guest anions of different type. The bigger cavities are filled with the octahedral MBr(6) (n-) ions (M=Cr or Fe; n=3 or 4), whereas the smaller cavities trap either Br- ions (1) or Hg(0) (2). The analysis of the host-guest contacts has allowed a classification of the octahedral guests as coordinated and the monatomic guests as clathrated. Magnetic measurements and ESR spectroscopy data have given information about the interaction between the host and guests. Band structure calculations (HF and hybrid DFT level) indicate that both 1 and 2 are non-metallic, with a band gap of approximately 1.5 eV (B3LYP), and that the interaction between the host and guests is of predominantly electrostatic character. It is shown that though the electrostatic host-guest interaction is weak it plays an important role in assembling the perfectly ordered supramolecular architectures.

Journal Article↗
PubMed2002

An ab initio theoretical study of electronic structure and properties of 2'-deoxyguanosine in gas phase and aqueous media.

Molecular geometries of two structural forms of 2'-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2'-endo and C3'-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2'-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2'-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water-air interface. Though the normal Watson-Crick-type base pairing would not be possible with the keto-N7R form of 2'-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti-conformation of 2'-deoxyguanosine including the dihedral angle chi(CN) agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2'-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H(+) and OH(-) fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH(-) group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2'-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2003

Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks.

A sparse matrix multiplication scheme with multiatom blocks is reported, a tool that can be very useful for developing linear-scaling methods with atom-centered basis functions. Compared to conventional element-by-element sparse matrix multiplication schemes, efficiency is gained by the use of the highly optimized basic linear algebra subroutines (BLAS). However, some sparsity is lost in the multiatom blocking scheme because these matrix blocks will in general contain negligible elements. As a result, an optimal block size that minimizes the CPU time by balancing these two effects is recovered. In calculations on linear alkanes, polyglycines, estane polymers, and water clusters the optimal block size is found to be between 40 and 100 basis functions, where about 55-75% of the machine peak performance was achieved on an IBM RS6000 workstation. In these calculations, the blocked sparse matrix multiplications can be 10 times faster than a standard element-by-element sparse matrix package.

Journal Article↗
PubMed2003

A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods.

A driver program for carrying out nudged elastic band optimizations of minimum energy reaction pathways is described. This approach allows for the determination of minimum energy pathways using only energies and gradient information. The driver code has been interfaced with the GAUSSIAN 98 program. Applications to two isomerization reactions and to a cluster model for H(2) desorption from the Si(100)-2 x 1 surface are presented.

Journal Article↗
PubMed2004

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry.

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system.

Journal Article↗
PubMed2006

Efficiency and accuracy of the elongation method as applied to the electronic structures of large systems.

Current state of development of the elongation method originally proposed by Imamura is presented. Recent progress in methodology, including geometry optimization and employment of the fast multiple method, is highlighted. The accuracy and efficiency of the elongation method as compared to exact canonical Hartree-Fock and Kohn-Sham approaches are discussed. Potential applications are illustrated by wide range of calculations for model systems. The elongation calculations are demonstrated to be much more efficient compared to the conventional ones with high accuracy maintained. The elongation CPU time is shown by the model calculations as linear or sub-linear scaling for quasi-one-dimensional systems. Future work of development into post-Hartree-Fock methodologies are pointed out.

Journal Article↗
PubMed1975

Electronic spectra and electronic structures of some antimicrobials derived from proflavine.

The shifts in the absorption and fluorescence spectra of 3-aminoacridine, proflavine, acridine orange, and acridine yellow were employed to show that the singly charged cations, the predominant species at biological pH, exist in the ground state in the amino form. In the lowest excited singlet state, however, the monocations of the diaminoacridines have the imino structure, a conclusion supported by the relative ground- and excited-state pKa values of the reactions of the monocation with H-+. The ground-state amino structure has its positive charge concentrated at the heterocyclic nitrogen atom, a fact that is of primary importance in determining the geometry of binding to DNA.

Acridines↗
PubMed2004

Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods.

The characterization of electrostatic and chemical properties at the surface of biological macromolecules is of interest in elucidating the fundamental biological structure-function relationships as well as in problems of rational drug design. This paper presents a set of macromolecular quantum descriptors for the characterization of biological macromolecules in solution that can be obtained with modest computational cost from linear-scaling semi-empirical quantum/solvation methods. The descriptors discussed include: solvent-polarized electrostatic surface potential maps, equilibrated atomic charges, Fukui reactivity indices, approximate local hardness maps, and relative proton potentials. These properties are applied to study the conformational dependence of the electrostatic surface potential of the solvated phosphate-binding protein mutant (T141D), the regioselectivity of the zinc finger domains of HIV-1 nucleocapsid (NC) protein, and the order of pKa values of acidic residues in turkey ovomucoid third domain (OMTKY3) and of the zinc-binding residues in the carboxyl terminal zinc finger of NC. In all cases, insight beyond that obtainable from purely classical models is gained and can be used to rationalize the experimental observations. The macromolecular quantum descriptors presented here greatly extend the arsenal of tools for macromolecular characterization and offer promise in applications to modern structure-based drug design.

Computational Biology↗
PubMedDate not supplied

Analytical and structural electron microscopy of chromium carcinogenesis in vitro.

Syrian hamster embryo cells have been grown in culture on thin (10-50 nm), evaporated substrates of chromium, and examined by analytical transmission electron microscopy. After 10 d exposure, significant metal uptake was observed and numerous cell colonies showed the physical characteristics of carcinogenic transformation. The majority of the ingested chromium appeared to be associated with nucleic acid complexes. As a control, cells grown on titanium showed no signs of metal uptake and had morphologies very similar to cells grown on conventional carbon substrates.

Animals↗