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1.
Mariusz P. Mitoraj Rafał Kurczab Marek Boczar Artur Michalak 《Journal of molecular modeling》2010,16(11):1789-1795
In the present study we have analyzed hydrogen bonding in dimer and trimer of oxalic acid, based on a recently proposed charge
and energy decomposition scheme (ETS-NOCV). In the case of a dimer, two conformations, α and β, were considered. The deformation
density contributions originating from NOCV’s revealed that the formation of hydrogen bonding is associated with the electronic
charge deformation in both the σ—(Δρσ) and π-networks (Δρπ). It was demonstrated that σ-donation is realized by electron transfer from the lone pair of oxygen on one monomer into the
empty rH - O* \rho_{H - O}^* orbital of the second oxalic acid fragment. In addition, a covalent contribution is observed by the density transfer from
hydrogen of H-O group in one oxalic acid monomer to the oxygen atom of the second fragment. The resonance assisted component
(Δρπ), is based on the transfer of electron density from the π—orbital localized on the oxygen of OH on one oxalic acid monomer
to the oxygen atom of the other fragment. ETS-NOCV allowed to conclude that the σ(O---HO) component is roughly eight times
as important as π (RAHB) contribution in terms of energetic estimation. The electrostatic factor (ΔEelstat) is equally as important as orbital interaction term (ΔEorb). Finally, comparing β-dimer of oxalic acid with trimer we found practically no difference concerning each of the O---HO
bonds, neither qualitative nor quantitative. 相似文献
2.
Mo Y 《Journal of molecular modeling》2006,12(5):665-672
Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol−1 at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol−1) and H-AT (−12.8 kcal mol−1) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.
Figure Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10−3 a.u.); b shows the charge transfer effect (isodensity 2×10−4 a.u.)
Dedicated to Professor Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
3.
We have systematically investigated the noncovalent and covalent adsorption of alanine and alanine radicals, respectively,
onto a (5, 0) single-walled carbon nanotube using first-principles calculation. It was found that XH···π (X = N, O, C) interactions
play a crucial role in the non-ovalent adsorption and that the functional group close to the carbon nanotube exhibits a significant
influence on the binding strength. Noncovalent functionalization of the carbon nanotube with alanine enhances the conductivity
of the metallic (5, 0) nanotube. In the covalent adsorption of each alanine radical onto a carbon nanotube, the binding energy
depends on the adsorption site on CNT and the electronegative atom that binds with the CNT. The strongest complex is formed
when the alanine radical interacts with a (5, 0) carbon nanotube through the amine group. In some cases, the covalent interaction
of the alanine radical introduces a half-filled band at the Fermi level due to the local sp
3 hybridization, which modifies the conductivity of the tube. 相似文献
4.
Christensen U 《Bioscience reports》2007,27(6):327-333
2′-O,4′-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid
analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity,
gene regulation and nucleic acid diagnostics seems promising. Here we show kinetic and thermodynamic results on the interaction
of a series of 10 bases long LNA–DNA mixmers, gabmers as well as full length LNA’s with the complementary DNA, RNA and LNA
oligonucleotides in the presence and absence of 10 mM Mg2+- ions. Our results show no significant differences in the reaction thermodynamics and kinetics between the LNA species, only
a tendency to stronger duplex formation with the gabmer and mixmer. Introduction of a few LNA’s thus may be a better strategy,
than using full length LNA’s to obtain an oligonucleotide that markedly increases the strength of duplexes formed with the
complementary DNA and RNA. 相似文献
5.
Olga Zakharieva Michael Grodzicki A. X. Trautwein Cees Veeger Ivonne M. C. M. Rietjens 《Journal of biological inorganic chemistry》1996,1(3):192-204
The reaction mechanism for the hydroxylation of benzene and monofluorobenzene, catalysed by a ferryl-oxo porphyrin cation
radical complex (compound) is described by electronic structure calculations in local spin density approximation. The active
site of the enzyme is modelled as a six-coordinated (Por+)Fe(IV)O a2u complex with imidazole or H3CS– as the axial ligand. The substrates under study are benzene and fluorobenzene, with the site of attack in para, meta and
ortho position with respect to F. Two reaction pathways are investigated, with direct oxygen attack leading to a tetrahedral
intermediate and arene oxide formation as a primary reaction step. The calculations show that the arene oxide pathway is distinctly
less probable, that hydroxylation by an H3CS––coordinated complex is energetically favoured compared with imidazole, and that the para position with respect to F is the
preferred site for hydroxylation. A partial electron transfer from the substrate to the porphyrin during the reaction is obtained
in all cases. The resulting charge distribution and spin density of the substrates reveal the transition state as a combination
of a cation and a radical σ-adduct intermediate with slightly more radical character in the case of H3CS– as axial ligand. A detailed analysis of the orbital interactions along the reaction pathway yields basically different mechanisms
for the modes of substrate–porphyrin electron transfer and rupture of the Fe–O bond. In the imidazole-coordinated complex
an antibonding π*(Fe–O) orbital is populated, whereas in the H3CS––coordinated system a shift of electron density occurs from the Fe–O bond region into the Fe–S bond.
Received: 1 July 1995 / Accepted: 18 December 1995 相似文献
6.
Muñoz-Muriedas J Barril X López JM Orozco M Luque FJ 《Journal of molecular modeling》2007,13(2):357-365
We investigate the changes in the solvation properties of the natural nucleic acid bases due to the formation of the canonical
Watson–Crick hydrogen-bonded complexes. To this end, the changes in the free energy of solvation of the bases induced upon
hydrogen-bonded dimerization are analyzed by means of the hydrophobic similarity index, which relies on the atomic contributions
to the free energy of solvation determined by the partitioning method implemented in the framework of the MST continuum model.
Such an index is also used to examine the hydrophobic similarity between the canonical nucleic acid bases and a series of
highly apolar analogues, which have been designed as potential candidates to expand the genetic alphabet. The ability of these
analogues to be incorporated into modified DNA duplexes can be related to the large reduction in the hydrophilicity of the
natural bases upon formation of the canonical hydrogen-bonded dimers. The results illustrate the suitability of the hydrophobic
similarity index to rationalize the role played by solvation in molecular recognition.
Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005. 相似文献
7.
Saito K Tai H Fukaya M Shibata T Nishimura R Neya S Yamamoto Y 《Journal of biological inorganic chemistry》2012,17(3):437-445
Abstract
The structure of a carbon monoxide (CO) adduct of a complex between heme and a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), has been characterized using 1H and 13C NMR spectroscopy and density function theory calculations. The study revealed that the heme binds to the 3′-terminal G-quartet of the DNA though a π–π stacking interaction between the porphyrin moiety of the heme and the G-quartet. The π–π stacking interaction between the pseudo-C 2-symmetric heme and the C 4-symmetric G-quartet in the complex resulted in the formation of two isomers possessing heme orientations differing by 180° rotation about the pseudo-C 2 axis with respect to the DNA. These two slowly interconverting heme orientational isomers were formed in a ratio of approximately 1:1, reflecting that their thermodynamic stabilities are identical. Exogenous CO is coordinated to heme Fe on the side of the heme opposite the G-quartet in the complex, and the nature of the Fe–CO bond in the complex is similar to that of the Fe–CO bonds in hemoproteins. These findings provide novel insights for the design of novel DNA enzymes possessing metalloporphyrins as prosthetic groups. 相似文献8.
Darío J. R. Duarte Margarita M. de las Vallejos Nélida M. Peruchena 《Journal of molecular modeling》2010,16(4):737-748
In this work, the intermolecular distribution of the electronic charge density in the aromatic hydrogen/halogen bonds is studied
within the framework of the atoms in molecules (AIM) theory and the molecular electrostatic potentials (MEP) analysis. The
study is carried out in nine complexes formed between benzene and simple lineal molecules, where hydrogen, fluorine and chlorine
atoms act as bridge atoms. All the results are obtained at MP2 level theory using cc-pVTZ basis set. Attention is focused
on topological features observed at the intermolecular region such as bond, ring and cage critical points of the electron
density, as well as the bond path, the gradient of the density maps, molecular graphs and interatomic surfaces. The strength
of the interaction increases in the following order: F⋅⋅⋅π < Cl⋅⋅⋅π < H⋅⋅⋅π. Our results show that the fluorine atom has the
capability to interact with the π−cloud to form an aromatic halogen bond, as long as the donor group is highly electron withdrawing.
The Laplacian topology allows us to state that the halogen atoms can act as nucleophiles as well as electrophiles, showing
clearly their dual character. 相似文献
9.
Fu-de Ren Duan-lin Cao Wen-liang Wang Jun Ren Su-qing Hou Shu-sen Chen 《Journal of molecular modeling》2009,15(5):515-523
The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid
hydrogen of HF, HCl, HCN and H2C2 using MP2 and B3LYP methods at 6-311++G(2df,2p) and aug-cc-pVTZ levels. The binding energies follow the order of HB=BH...HF>HB=BH...HCl>HB=BH...HCN>HB=BH...H2C2. The hydrogen-bonded interactions in HB=BH...HX are found to be stronger than those in H2C=CH2...HX and OCB≡BCO...HX. The analyses of natural bond orbital (NBO) and the electron density shifts reveal that the nature
of the T-shaped X–H...π hydrogen-bonded interaction is that much of the lost density from the π-orbital of B=B bond is shifted
toward the hydrogen atom of the proton donor, leading to the electron density accumulation and the formation of the hydrogen
bond. The atoms in molecules (AIM) theory have also been applied to characterize bond critical points and confirm that the
B=B double bond can be a potential proton acceptor.
The unusual T-shaped X–H...π hydrogen bonds are found between the B=B double bond of the singlet state HB=BH and the acid
hydrogen of HF, HCl, HCN and H2C2 相似文献
10.
Cell adhesion molecules are important for their various roles in many cellular events and responses. In the present study,
we have analyzed the roles played by cation–π interactions in the structural stability of adhesion molecules. These interactions are mainly formed by long-range contacts.
The occurrence of arginine is higher than lysine to form cation–π interactions. The secondary structure preferences of interacting residues are independent of amino acid class. Cation–π interactions might stabilize the interface between the terminus and core in this class of proteins. The results obtained
in the present study will be useful in understanding the contribution of cation–π interactions to the overall stability of adhesion proteins. 相似文献
11.
Yury V. Rubin Leonid F. Belous Аnatolij А. Yakuba 《Journal of molecular modeling》2011,17(5):997-1006
To study M-DNA molecular structure (such DNA with transition metal ions placed between the nucleic bases is able to conduct
the electric current) and its conductivity mechanisms, we carried out ab initio quantum-mechanical calculations of electronic and spatial structures, thermodynamic characteristics of adenine-thymine (АТ)
and guanine-cytosine (GC) base pair complexes with Zn2+ and Ni2+. To take into account the influence of the alkaline environment, calculations for these complexes were also carried out with
hydroxyl and two water molecules. Computations were performed at MP2 level of theory using 6–31+G* basis set. Analogous calculations
were carried out for (AC)(TG) stacking dimer of nucleic acid base pairs with two Zn2+. The calculation of the interaction energy in complexes has shown the preference of locating the metal ion (instead of the
imino proton) between bases in M-DNA. The electronic transition energy calculation has revealed the reduction of the first
singlet transition energy in АТ and GC complexes with Ni2+ from 4.5 eV to 0.4 - 0.6 eV. Ni2+ orbitals take part in the formation of HOMO and LUMO on the complexes investigated. It was shown that charges of metal ions
incorporated into complexes with nucleic bases and in dimer decrease significantly. 相似文献
12.
A nanohybrid adduct of the widely used, functional dye, daunomycin (DM), with single-walled carbon nanotubes (SWNTs) was prepared.
Ultraviolet-visible-near infrared and fluorescence spectroscopy and electrochemistry of DM-functionalized SWNTs reveal that
DM interacts with SWNTs through strong π–π stacking and there is a significant photo-induced charge-transfer interaction between
the two components. Importantly, the novel adduct modified the glassy carbon (GC) electrode to give a much enhanced electrochemical
activity than those of DM adsorbed onto not only the bare GC electrode but also the SWNTs-modified GC electrode. 相似文献
13.
The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded
and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and
C6H6 is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies
in the case of XOH–C6H6 complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids.
Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in
benzene. 相似文献
14.
The paper presents a set of two-dimensional experiments that utilize direct 13C detection to provide proton–carbon, carbon–carbon and carbon–nitrogen correlations in the bases of nucleic acids. The set
includes a 13C-detected proton–carbon correlation experiment for the measurement of 13C–13C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the 13C–13C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton
with a network of coupled carbons, and a 13C-detected 13C–15N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used
for extracting the carbon–carbon couplings and/or carbon decoupling in the direct dimension, while the S3E procedure is preferred in the indirect dimension of the carbon–nitrogen experiment to obtain the value of the coupling constant.
The experiments supply accurate values of 13C and 15N chemical shifts and carbon–carbon and carbon–nitrogen coupling constants. These values can help to reveal structural features
of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
15.
Vassil B. Delchev 《Journal of molecular modeling》2010,16(4):749-757
Six uridine and six deoxyuridine isomers were studied at the B3LYP and TD B3LYP theoretical level and 6–31+G(d) basis function.
The stability and the excited states of the isomers were studied in order to clarify some known experimental data. It was
established that the rotation of the oxo uracil ring in uridine is energetically more likely to occur in the excited state
than in the ground state, driven by the bright 1
ππ* state and the dark charge transfer 1nπ* state. Very high energy barriers (on the So) were found for thermal intramolecular proton transfer processes. 相似文献
16.
Latosińska JN Latosińska M Tomczak MA Seliger J Zagar V 《Journal of molecular modeling》2011,17(7):1781-1800
The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were
studied experimentally in the solid state via 35Cl NQR, 1H-17O and 1H-14N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O–H···N
hydrogen bonds linking dimers and π–π stacking interactions were described within the QTAIM (quantum theory of atoms in molecules)
/DFT (density functional theory) formalism. Both proton donor and acceptor sites in O–H···N bonds were characterized using
1H-17O and 1H-14N NQDR spectroscopies and QTAIM. The possibility of the existence of O–H···H–O dihydrogen bonds was excluded. The weak intermolecular
interactions in the crystals of clioquinol and cloxiquine were detected and examined. The results obtained in this work suggest
that considerable differences in the NQR parameters for the planar and twisted supramolecular synthons permit differentiation
between specific polymorphic forms, and indicate that the more planar supramolecular synthons are accompanied by a greater
number of weaker hydrogen bonds linking them and stronger π···π stacking interactions. 相似文献
17.
Rehab F. Abdelhamid Yuji Obara Yoshiko Uchida Takamitsu Kohzuma David M. Dooley Doreen E. Brown Hiroshi Hori 《Journal of biological inorganic chemistry》2007,12(2):165-173
Noncovalent weak interactions play important roles in biological systems. In particular, such interactions in the second coordination
shell of metal ions in proteins may modulate the structure and reactivity of the metal ion site in functionally significant
ways. Recently, π–π interactions between metal ion coordinated histidine imidazoles and aromatic amino acids have been recognized as potentially
important contributors to the properties of metal ion sites. In this paper we demonstrate that in pseudoazurin (a blue copper
protein) the π–π interaction between a coordinated histidine imidazole ring and the side chains of aromatic amino acids in the second coordination
sphere, significantly influences the properties of the blue copper site. Electronic absorption and electron paramagnetic resonance
spectra indicate that the blue copper electronic structure is perturbed, as is the redox potential, by the introduction of
a second coordination shell π–π interaction. We suggest that the π–π interaction with the metal ion coordinated histidine imidazole ring modulates the electron delocalization in the active site,
and that such interactions may be functionally important in refining the reactivity of blue copper sites.
Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. 相似文献
18.
19.
The molecular structures and absorption spectra of triphenylamine dyes containing different numbers of anchoring groups (S1-S3)
were investigated by density functional theory (DFT) and time-dependent DFT. The calculated geometries indicate that strong
conjugation is formed in the dyes. The interfacial charge transfer between the TiO2 electrode and S1-S3 are electron injection processes from the excited dyes to the semiconductor conduction band. The simulated
absorption bands are assigned to π → π* transitions according to the qualitative agreement between the experimental and calculated
results. The effect of anchoring group number on the molecular structures, absorption spectra and photovoltaic performance
were comparatively discussed. 相似文献
20.
Srđan Đ. Stojanović Vesna B. Medaković Goran Predović Miloš Beljanski Snežana D. Zarić 《Journal of biological inorganic chemistry》2007,12(7):1063-1071
Searching structures of porphyrin-containing proteins from the Protein Data Bank revealed that the π system of every porphyrin ring is involved in XH/π interactions, with most of the porphyrins having several interactions. Both five-membered pyrrole rings and six-membered
chelate rings are involved in XH/π interactions; the number of interactions with five-membered rings is larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as hydrogen-atom donors; however, the number of CH/π interactions is much larger than the number of NH/π interactions. The amino acids involved in the interactions show a high conservation score. Our results that every porphyrin
is involved in XH/π interactions and that amino acids involved in these interactions are highly conserved demonstrate that XH/π interactions play an important role in porphyrin–protein stability.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献