Structure and Stability of DNA Base Trimers:  An Electrostatic Approach

Pundlik, Savita S.; Gadre, Shridhar R.

doi:10.1021/jp972491o

Cited by 51 publications

(45 citation statements)

References 38 publications

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“…Similarly the Lewis acid properties of triel centers analyzed here may be explained in terms of EP. One can mention other important studies, as for example, on the role of EP in the hydratation process or on the stability of DNA dimers and trimers …”

Section: Resultsmentioning

confidence: 99%

Two faces of triel bonds in boron trihalide complexes

Grabowski

2017

J Comput Chem

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The N⋅⋅⋅B triel bonds in complexes of boron trihalides, BX (X = F, Cl, Br, and I), with species acting as Lewis bases through the nitrogen center, NH , N , and HCN, are analyzed theoretically (MP2/aug-cc-pVTZ calculations). It is confirmed that stronger Lewis acid properties of the boron center are observed for the BCl moiety than for the BF one in complexes with the strong Lewis base (NH ); while the opposite order is observed for complexes with the weak Lewis base (N ). The BX NCH complexes (for X = Cl, Br, and I) are characterized by two tautomeric forms and by two corresponding N⋅⋅⋅B distances, the shorter one possesses characteristics of the covalent bond. In a case of the BF NCH complex one energetic minimum is observed. Ab initio calculations are supported by an analysis of molecular electrostatic potentials (EPs) and electron density distributions. The quantum theory of 'atoms in molecules' and the decomposition of the energy of interaction are applied. The aforementioned acidity orders as well as the existence of two tautomers for some of complexes result partly from the electrostatic interactions' balance; the EP distribution is different for the BF species than for the other BX species where X = Cl, Br, and I. © 2017 Wiley Periodicals, Inc.

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Section: Resultsmentioning

confidence: 99%

Two faces of triel bonds in boron trihalide complexes

Grabowski

2017

J Comput Chem

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“…This interaction energy is minimized by rotating and translating the guest molecule such that the van der Waals surfaces of the guest and the host do not interpenetrate. The EPIC model was applied successfully to many systems such as DNA base dimers and trimers [86], hydration of crown ether [87] and stacked and H-bonded cytosine dimer [88]. Previous studies performed in our laboratory generally demonstrated striking similarities between the geometries obtained from ab initio and EPIC calculations.…”

Section: Use Of Molecular Electrostatic Potential For Probing Lone Pamentioning

confidence: 79%

“…This electrostatic picture brings out the reason why electron rich species interact attractively with π -deficient aromatic systems. Based on electrostatics and its topographical features, Gadre et al [85,86] developed a model several years' ago, named as electrostatic potential for intermolecular complexation (EPIC), which provides a simple tool for estimating the interaction energy and geometry of the weakly interacting molecular species. In this model, the interaction energies are calculated by summing the MESP driven point charges q A,i of the guest molecule multiplied with the electrostatic potential value of the host at the location of the point charge and vice versa.…”

Section: Use Of Molecular Electrostatic Potential For Probing Lone Pamentioning

confidence: 99%

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

Gadre

Kumar

2015

Challenges and Advances in Computational Chemistry and Physics

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Over the last two decades, studies on lone pair-π interaction have attracted lot of attention of experimental as well as theoretical chemists due to its intriguing nature and its suspected presence in biological systems. The present Chapter begins with a brief overview of the earlier theoretical and experimental work done in this area. This is followed by exploration of the nuances of bonding in lone pair-π interaction, employing the tool of molecular electrostatic potential (MESP) since such weak interactions are mainly dominated by electrostatic features of host and guest molecules. The critical points associated with the scalar field of MESP are exploited for scrutinizing the directionality and bonding sites involved in the lone pair-π complexes. Furthermore, the electrostatic potential for intermolecular complexation (EPIC) model developed by Gadre et al., has been employed for finding out the electrostatically optimized structures and interaction energies of these complexes. The outcomes of EPIC model are compared with the results obtained from quantum chemical calculations of the complexes employing M06L/6-311++G(d,p) level of theory. The present study details out four different cases of lone pair-π complexes, which are currently in vogue. Hexafluorobenzene, one of the most explored π -deficient host in the present context, is initially taken up to demonstrate various facets of MESP for gaining insights into this interaction. This is followed by the scrutiny of special classes of recently synthesized highly π -deficient molecules, viz. tetraoxacalix [2]arene[2]triazine and naphthalenediimide, which are known to have specificity and large affinity, respectively, towards the electron rich species. The chapter ends with the description of lone pair-π interaction in the case of urate oxidase, an enzyme present in biological systems.

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“…The interactive energies of the multimers have been calculated with Hartree-Fock, 39 DFT, [40][41][42]43,44 methods, to be used to examine our RM1 BH . Fortunately, there exist some experimental trimerization energies estimated by analyzing mass spectral peak intensities in multicomponent mixtures.…”

Section: Some Multimers Among Base(s) And/or Amino Acid Residue(s)mentioning

confidence: 99%

Can Semiempirical Quantum Models Calculate the Binding Energy of Hydrogen Bonding for Biological Systems?

Feng

Wang

Fang

et al. 2009

J. Theor. Comput. Chem.

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A modified semiempirical model named RM1 BH , which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1 BH is formulated by adding Gaussian functions to the core-core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1 BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller-Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1 BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

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Structure and Stability of DNA Base Trimers: An Electrostatic Approach

Cited by 51 publications

References 38 publications

Two faces of triel bonds in boron trihalide complexes

Two faces of triel bonds in boron trihalide complexes

Understanding Lone Pair-π Interactions from Electrostatic Viewpoint

Can Semiempirical Quantum Models Calculate the Binding Energy of Hydrogen Bonding for Biological Systems?

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