Complementary Electrostatics for the Study of DNA Base-Pair Interactions

Gadre, Shridhar R.; Pundlik, Savita S.

doi:10.1021/jp9640641

Cited by 74 publications

(50 citation statements)

References 45 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%

“…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. [64][65][66][67][68][69] Table 3 presents maximal and minimal values of EP for the boron trihalides, BX 3 , for molecular surfaces of the electron density of 0.001 au. The latter value was proposed earlier as that one which approximately corresponds to the van der Waals surface.…”

Section: The Ep For Boron Trihalidesmentioning

confidence: 99%

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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%

Section: The Ep For Boron Trihalidesmentioning

confidence: 99%

Two faces of triel bonds in boron trihalide complexes

Grabowski

2017

J Comput Chem

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“…The identification of such local features provides a useful tool for interpreting various non-covalent interactions such as tetrel, chalchogen, halogen and hydrogen bondings, as demonstrated by Politzer, Murray et al [20][21][22];  predictive approach. Among other approaches [28,29], we can mention the electrostatic potential for intermolecular complexes (EPIC) model of Pundlik et al [30]. This model allows the study of weakly bond complexes between two species based on the calculation of the electrostatic interaction energy.…”

Section: Introductionmentioning

confidence: 99%

A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

2017

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Encapsulation of small (bio-)organic molecules within water cages is governed by a subtle equilibrium between water-water and water-solute interactions. The competition between the formation of exohedral and endohedral complexes is investigated. The first step prior to a theoretical characterization of interactions involved in such complexes lies in the judicious choice of a level of theory. The β-propiolactone (BPL), a solute for which the micro-hydration was recently characterized by means of high resolution microwave spectroscopy (Angew. Chem. 2015, 127, 993), was selected for the present study, and a calibration step is carried out. It is shown that the dispersion-corrected density functional theory (DFT-D) suitably reproduce the geometric, energetic and spectroscopic features of the BPL:(H 2 O) 1-5 complexes. The experimentally-deduced structures of the BPL:(H 2 O) 4,5 species are fully understood in terms of the maximization of interactions between complementary sites in the MESPs. DFT-D calculations followed by the topological analysis within the Quantum Theory of Atoms in Molecules framework have shown that the solute could efficiently interact with (H 2 O) 6,10 clusters in a similar manner that the (H 2 O) 4,5 clusters do. The interaction of the solute with two larger water clusters is further investigated. The exohedral and endohedral BPL:(H 2 O) 20 isomers are close in energy with each other, whereas the formation of an inclusion complex is energetically more favored than the facial interaction in the case of the BPL:(H 2 O) 24 cluster. The topological analysis suggests that the substantial energetic stability is due to interactions between the solute and almost all oxygen atoms of the water cage.

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“…Some of the earlier models, which make use of the MESP as a basic parameter for studying clusters, include Buckingham–Fowler model 12, molecular mechanics for clusters 13, and Alhambra, Luque, and Orozco model 14. An MESP‐based model 15 developed earlier in our laboratory for studying weak interaction is electrostatic potential for intermolecular complexation (EPIC). This model has been employed for studying several homo‐ and hetero‐molecular complexes 16.…”

Section: Introductionmentioning

confidence: 99%

Ab initio study on (CO₂)_nclusters via electrostatics‐ and molecular tailoring‐based algorithm

Jose

Gadre

2009

Int J of Quantum Chemistry

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An algorithm based on molecular electrostatic potential (MESP) and molecular tailoring approach (MTA) for building energetically favorable molecular clusters is presented. This algorithm is tested on prototype (CO 2 ) n clusters with n ϭ 13, 20, and 25 to explore their structure, energetics, and properties. The most stable clusters in this series are seen to show more number of triangular motifs. Many-body energy decomposition analysis performed on the most stable clusters reveals that the 2-body is the major contributor (Ͼ96%) to the total interaction energy. Vibrational frequencies and molecular electrostatic potentials are also evaluated for these large clusters through MTA. The MTA-based MESPs of these clusters show a remarkably good agreement with the corresponding actual ones. The most intense MTA-based normal mode frequencies are in fair agreement with the actual ones for smaller clusters. These calculated asymmetric stretching frequencies are blue-shifted with reference to the CO 2 monomer. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2243 FIGURE 8. A comparison of MESP isosurfaces at Ϫ0.014 a.u. evaluated through [A] MTA and [B] actual whole cluster calculation of (CO 2 ) 13 and (CO 2 ) 20 clusters. See Table III and text for details.

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Complementary Electrostatics for the Study of DNA Base-Pair Interactions

Cited by 74 publications

References 45 publications

Two faces of triel bonds in boron trihalide complexes

Two faces of triel bonds in boron trihalide complexes

A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

Ab initio study on (CO₂)_nclusters via electrostatics‐ and molecular tailoring‐based algorithm

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Complementary Electrostatics for the Study of DNA Base-Pair Interactions

Cited by 74 publications

References 45 publications

Two faces of triel bonds in boron trihalide complexes

Two faces of triel bonds in boron trihalide complexes

A theoretical investigation of water–solute interactions: from facial parallel to guest–host structures

Ab initio study on (CO2)nclusters via electrostatics‐ and molecular tailoring‐based algorithm

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Ab initio study on (CO₂)_nclusters via electrostatics‐ and molecular tailoring‐based algorithm