A theoretical study of the interaction of monomethylammonium with double-stranded oligonucleotides

Theoretical computations are performed of the interaction specificities of the monomethylammoniumion with double-stranded oligonucleotides (dPu)_n·(dPy)_n in the B-DNA conformation. The effects of base sequence and chain length are examined. In short oligomers (n = 2, 3), the interaction energies of the cation are larger in the major groove of (dG)_n·(dC)_n than in the minor groove of (dA)_n·(dT)_n. As a consequence of further shaping of the grooves and building up of the phosphates, a marked reversal in the affinities of the cation for the grooves occurs at the (dPu)₅·(dPy)₅ and the p(dPu)₅p·p(dPy)₅p levels: it is the binding in the minor groove of the adenine-thymine oligomers that provides then the most favorable interaction energies. It is also shown, at the level of the double helices built from dinucleoside monophosphates, that the interaction of monomethylammonium in the minor groove occurs in specific configurations involving the three NH bonds of the cation, and two successive bases on one strand; this binding is sequence-specific, the order of inherent preferences being (TpA) > (TpT) > (ApA) > (ApT).     

Theoretical study of binding of tetramethylammonium ion with aromatics

Ab initio computations including correlation have been performed in a comparative study of complexes of tetramethylammonium (TMA) with benzene, pyrrole, pyridine, and imidazole, using polarized Gaussian basis sets of different accuracies. With the best basis (optimized on molecular polarizabilities), the BSSE-corrected binding energies in the most stable complexes of these four ligands are 9.1, 10.7, 13.3, and 16.3 kcal/mol, respectively, with benzene and pyrrole binding in a plane perpendicular to the TMA axis, and pyridine and imidazole inserting their nitrogen lone pair essentially along the TMA axis. The characteristics of secondary sites of binding of benzene are also determined and the overall results are discussed in connection with the possible role of aromatic amino acids in proteins. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2012–2022, 1997     

Theoretical and experimental study of montmorillonite intercalated with tetramethylammonium cation

Structural and vibrational features of Na-montmorillonite and montmorillonite intercalated with tetramethylammonium cation (TMA⁺) were characterized theoretically and experimentally. Theoretical study was performed using density functional theory with inclusion of dispersion corrections. The analysis of the hydrogen bonds in the calculated models has shown that the Na⁺ cations coordinated by six water molecules (Na-M model) are bound to montmorillonite layers by moderate hydrogen bonds between water molecules and basal oxygen atoms of the tetrahedral sheets. Hydrated Na⁺ cations are stabilized by relatively strong hydrogen bonds among water molecules. In the intercalate model, the TMA⁺ cation is fixed in the interlayer space by weak hydrogen bonds between the methyl groups and basal oxygen atoms of montmorillonite layers. The calculated vibrational spectra are in a good agreement with the measured infrared spectra. The detailed analysis of the simulated vibrational spectra allowed unambiguous identification of corresponding bands in the measured spectra and their assignment to the particular vibrational modes. For example, calculations clearly distinguished between AlMgOH and AlAlOH stretching vibrations and also between the coupled vibrations of the methyl groups of the TMA⁺ cations.     

An approach to the ionic cholinergic interaction. Theoretical treatment of the interaction between tetramethylammonium and acetate ions

The interaction between the anionic site of cholinesterase and the cationic end of acetylcholine is estimated by considering a simplified model. The effect of the aqueous environment on the stability of the aggregate is considered.     

Theoretical study of the interaction of molecular oxygen with copper clusters

A new method based on frontier orbital theory has been used to investigate the binding site of molecular oxygen to neutral and anion copper clusters. It has been shown that one can make useful predictions of the binding sites based on the knowledge of the donor local reactivity of the cluster using the condensed Fukui function, f(-)(Ff). In this way, it was found that Cu(3), Cu(5), and Cu(5)(-) have the highest reactivity toward molecular oxygen.     

A spectrophotometric study on the interaction of neutral red with double-stranded DNA in large excess

With the measurement of molecular absorption, the interaction of neutral red (NR) with double-stranded DNA in large excess was investigated. It was found that the interaction of NR, existing in the acidic state (HNR) at pH 4.56, with double-stranded structure DNA displays different spectral features depending on the molar ratio of HNR/DNA, R. If R>1.33, the binding process is characterized by a binding constant at the 10(6) level with each nucleotide residue of double-stranded DNA binding one HNR molecule. If R<0.67, the binding constant is reduced to the 10(4) level, and the binding number for each nucleotide residue of double-stranded DNA to HNR is less than one.     

吡啶-BH~3相互作用复合物的理论研究

对吡啶-BH~3复合物分别用MP2/6-31+G^*和B3LYP/6-31+G^*进行理论计算以预测该复合物的构型及解离能，得到四种构型，在MP2优化构型基础上作CCSD/6-31+G^*单点能量计算以验证MP2与B3LYP结果的可靠性，然后用B3LYP作振动频率分析，计算了各构型的垂直电离势，最后用更大基组作单点能量计算和自然键轨道(NBO)分析。结果表明，N-B直接相连的构型最稳定，其解离能为141.50kJ/mol,MP2和B3LYP对N-H接近的构型结果相关较大，另外两种构型稳定性介于二者之间，解离能分别为15.18kJ/mol,14.06kJ/mol(MP2/6-31+G^*)。     

Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA

Cationic porphyrin derivatives such as meso-tetrakis(4-N-methylpyridinium)porphyrin, TMPyP, have been shown to interact with double-stranded DNA. The manganese derivative, Mn(III)-TMPyP, activated by an oxygen donor like potassium monopersulfate, provides an efficient DNA-cleaving system. Previous experimental work1 has shown that DNA cleavage by the Mn(III)-TMPyP/KHSO(5) system was due to an oxidative attack, within the minor groove of B-DNA, at the C5' or C1' carbons of deoxyribose units. The aim of this study was to use molecular modeling to elucidate the specificity of the interactions between the transient active species oxyl-Mn(IV)-TMPyP and the DNA target. Geometric parameters, charges, and force field constants consistent with the AMBER 98 force field were calculated by DFT methods. Molecular modeling (mechanics and dynamic simulations) were performed for oxyl-(hydroxo)-Mn(IV)-TMPyP bound in the minor groove of the dodecamer d(5'-TCGTCAAACCGC)-d(5'-GCGGTTTGACGA). Geometry, interactions, and binding energy of the metalloporphyrin located at the A.T triplet region of the dodecamer were analyzed. These studies show no significant structural change of the DNA structure upon ligand binding. Mobility of the metalloporphyrin in the minor groove was restrained by the formation of a hydrogen bond between the hydroxo ligand trans to the metal-oxyl and a DNA phosphate, restricting the access of the oxyl group to the (pro-S) H atom at C5'.     

A Theoretical study of the interaction of ethylene with transition metal complexes

In order to be able to describe the ethylene molecule bonded to an active site of a Titanium- or Nickel fluoride crystal, we have used the Hartree-Fock-Slater model, implemented by a Discrete Variational Method, as introduced by Ellis and Painter. The study of the ethylene molecule at a crystal surface then gives a clear, easily interpreted picture of the electronic structure. The-back donation from metal to olefin is found to be extremely important, both in the Ti- and in the Ni-complex. This back donation is caused by a strong interaction of ad orbital of the central ion with a ^* as well as the ^* molecular orbital of ethylene. As a result of these interactions, the C-C bond of ethylene is weakened considerably.A comparison is made between the Ti-ethylene and the Ni-ethylene systems.

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Zusammenfassung Die Elektronenstruktur von Äthylen, das an ein aktives Zentrum eines Titan- bzw. Nickelfluoridkristalls gebunden ist, ist mittels der Hartree-Fock-Slater-Theorie kombiniert mit der sog. Discrete Variational Method theoretisch behandelt worden. Es zeigt sich, daß die-Backdonation sowohl im Nickel- als auch im Titankomplex außerordentlich wichtig ist; sie entsteht durch eine starke Wechselwirkung eines Metall-d-Orbitals sowohl mit einem ^* als auch einem ^*-Orbital des Äthylens. Dies führt zu einer erheblichen Schwächung der Doppelbindung.Außerdem werden die beiden Systeme (Titan und Nickel) miteinander verglichen.

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Alfred P. Sloan Research Fellow     

A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA

The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 x 10(-5) and 2 x 10(-4), respectively. However, upon binding to double-stranded DNA, large spectroscopic changes result and the quantum yield of fluorescence is enhanced by four orders of magnitude, reaching values up to phi F = 0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The two derivatives also bind with single-stranded oligonucleotides, but the fluorescence quantum yield is not so great as that when bound to double-stranded samples. Typical fluorescence quantum yields of 7 x 10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas the fluorescence quantum yield remains below 10(-2) when interacting with single-stranded oligonucleotides. This slight but significant quantum-yield increase is interpreted as a folding of the single strand around the dye, which reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properties, it is proposed to link monomer covalently to oligonucleotides for the subsequent detection of target sequences within cells.     

Theoretical study of the Au–ethylene interaction

The basis‐set dependence and quasirelativistic and nonrelativistic effects on the Au C₂H₄ interaction are examined at the ab initio level. The effects on the interaction energies are modulated by f‐type polarization orbitals, using 19‐VE quasirelativistic pseudopotentials. Oscillation in the equilibrium Au C distance as well as in the interaction energy are sensitive to the electron correlation potential. These effects are evaluated at several levels of theory, ranging from MP2 to CCSD(T). The nature of the Au C₂H₄ interaction is related to a simple dispersion expression involving the individual properties of each component and its long‐distance behavior. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 317–324, 1999     

Theoretical study on Pd dimer and trimer interaction with the hydrogen molecule

The H₂ interaction with the Pd dimer and trimer were studied using multiconfigurational self-consistent field (MC-SCF) calculations with the relativistic effective core potential (RECP); the correlation energy correction was included in the extended multireference configuration interaction (MRCI), variational and perturbative to second order. Here, we considered the Pd₂ first six states: ³Σ⁺_u, ¹Σ⁺_g, ³Π_g, ³Δ_xy, ¹Σ⁺_u, and ³Σ⁺_g. For them, the four geometrical approaches included were the side-on H₂ toward Pd₂, for the hydrogen molecule in and out the Pd dimer plane; the perpendicular end-on H₂ toward Pd₂; and the perpendicular end-on Pd₂ to H₂. The Pd₂ ground state is ³Σ⁺_u, which only captures H₂ in the C_2v end-on approach, softly relaxing the H(SINGLE BOND)H bond. The closed-shell ¹Σ⁺_g captures the H₂ molecule in all the approaches considered: The side-on approach of this state presents deep wells and relaxes the H(SINGLE BOND)H bond, and the end-on approach captures H₂ with a relatively longer H(SINGLE BOND)H distance and also a deep well. The ³Π_g state was the only one which did not capture H₂. For the triangular Pd₃ clusters, H₂ was approached in the C_2v symmetry in and out of the Pd₃ plane. In the triangular case, H₂ was absorbed in both spin states, with deep wells and relaxing the H(SINGLE BOND)H distance. The linear Pd₃ singlet and triplet states capture outside of the Pd₃ and break the H(SINGLE BOND)H bond. © 1997 John Wiley & Sons, Inc.     

Theoretical study of the interaction of carbon monoxide with 3d metal dimers

The interaction of carbon monoxide with 3d metal dimers (scandium through zinc) has been examined using six different exchange-correlation density functionals. Results are compared to the relevant experimental values and to other theoretical investigations when available, and the overall agreement has been obtained. The BP86 functional gives calculated C-O stretching vibrational frequencies much closer to the experimental values than the B3P86, B3LYP, mPW1PW91, and PBE1PBE functionals, and furthermore, replacing the correlation part by the Lee-Yang-Parr correlation functional yields essentially the same results. It is generally found that on going from left to right across the 3d metal series, the preference for geometrical configuration is from side-on-bonded mode to bridging, and then to terminal, whereas Ni(2)CO adopts bridging mode. Particularly, the present computation reveals a significant tendency toward four-electron donor carbonyl groups with metal-oxygen bonds with the early transition metals scandium and titanium. The C-O stretching vibrational frequencies in the ground states of M(2)CO (M=Sc to Zn) increase generally from the left to the right side of the Periodic Table. The binding energies exhibit an overall decrease trend. These general trends in the interaction of carbon monoxide with 3d metal dimers mirror the main features of CO adsorption on transition metal surfaces.     

Theoretical study on intermolecular interaction of epoxyethane dimer

Ab initio calculations at Hartree–Fock and fourth‐order Mø ller–Plesset (MP4) correlation correction levels with 6‐31G* basis set have been performed on the epoxyethane dimer. Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero‐point energy. The greatest corrected dimer binding energy is −8.36 kJ/mol at the MP4/6‐31G*//HF/6‐31G* level. The natural bond orbital analysis has been performed to trace the origin of the weak interactions that stabilize dimer. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 94–98, 2000     

Theoretical study of the interaction between LiNH2 and HMgH

The lithium bond between HMgH and LiNH₂ has been predicted and characterized with quantum chemical calculations at the MP2/6‐311++G(d,p) level. Upon formation of the lithium bond, both the Mg? H and Li? N bonds are stretched. The Li? N bond undergoes a red shift, whereas the Mg? H bond exhibits a blue shift. The lithium‐bonded complex is controlled mainly by electrostatic and polarization interactions. The binding energy of HMgH with LiNH₂ is computed to be 12.47 kcal/mol. The binding of the two molecules is enhanced by the substitution with the methyl group in the Li acceptor, whereas it is weakened by the replacement with whether the electron‐withdrawing group such as F, Cl, CN, NC, or the electron‐donating group (OH and HN₂). A negative cooperativity is present in the ternary system of 2LiNH₂ and HMgH. The polarization interaction plays an important role in the negative cooperativity. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of the interaction of nonactin with Na+, K+, and NH

In an attempt to account for the preferential binding to nonactin of K⁺ relative to Na⁺, theoretical computations are performed using the intermolecular interaction energies of the ionophore with the two cations. Both K⁺ and Na⁺ liganding conformations are considered, and an evaluation is made of the intramolecular energy expenditure caused by the reduction of the size of the cavity. The energy balance for the complexation of the two cations computed by taking into account the cation–ionophore interactions, the interactions between the liganding groups, as well as the desolvation enthalpies of the cations in methanol, favors K⁺ over Na⁺ by 4 to 5 kcal/mol, in fair agreement with the difference in the measured enthalpies of binding. The binding of NH to nonactin is also investigated.     

Theoretical study of the shifts of electronic spectra from solute-solvent interaction

Previous theories of spectral solvent shifts are briefly discussed. The basic dipole approximation is analyzed both theoretically and in relation to experimental information. On account of the restricted validity of this approximation — especially for molecules consisting of several polar groups — another, electrostatic model, originating from the Born charging, is investigated. This model is applied to semi-empirical PPP-calculations of spectral solvent shifts of some quinones. Among other things, this model predicts that not only n → π⁸ transitions may be blue shifted but also certain π → π* transitions. When the electrostatic effect is small, other terms may be responsible for the solvent shift, e.g. polarizability. The cavity effect is not expected to be important in the present context.     

Theoretical study of the interaction between selected adhesives and oxide surfaces

We investigate the competition of the various organic components of two representative adhesive systems for reactive defect sites at model surfaces of both SiO2 and Al2O3. The reaction energies of resin monomers, curing agents, and in some cases also of additional adhesion promoters with the defects are calculated. We applied a density-functional based tight-binding method including a self-consistent correction of the Mulliken charges, which has already proven to be a useful tool for computational materials science, delivering reliable structural and energetic information.