Electrostatic Potential Maps and Natural Bond Orbital Analysis: Visualization and Conceptualization of Reactivity in Sanger’s Reagent

Mottishaw, Jeffery D.; Erck, Adam; Kramer, Jordan H.; Sun, Haoran; Koppang, Miles D.

doi:10.1021/ed5006344

Cited by 49 publications

(29 citation statements)

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“…Molecular electrostatic potential maps Molecular electrostatic potential maps are very helpful in identifying the electron rich and electron deficient regions present in a molecule and have been employed extensively in different studies. 87,88 As established from previous studies, the magnitude of the electropositive region will be maximum on P atoms along the X-P bond. 89 Fig.…”

Section: Resultsmentioning

confidence: 64%

“Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds

Shukla

Chopra

2016

Phys. Chem. Chem. Phys.

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In this article, we have analyzed the nature and characteristics of PSe noncovalent interactions by studying the effect of substitution on XH2PSeH2, H3PSeHX and XH2PSeHX (X= -H, -F, -CH3, -CF3, -Cl, -OH, -OCH3, -NH2, -NHCH3, and -CN) as our systems of interest at MP2/aug-cc-pVDZ level of theory. Binding energy calculations depict that binding energy increases in the order XH2PSeH2 < H3PSeHX < XH2PSeHX with the nature of the substituent having a direct effect on the strength of the interactions. PSe contacts as short as 2.52 Å were observed and analyzed in our study. The energy values for PSe contacts were found to exist in the range of -1.20 kcal mol(-1) to -7.89 kcal mol(-1). The topological analysis confirms the presence of PSe contacts in all the complexes with characteristics similar to hydrogen bonds. NBO analysis helped in categorizing these interactions into pnicogen and chalcogen bonds, depending on the strength of P(lp) to σ*(Se-X) orbitals or Se(lp) to σ*(P-X) orbitals.

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Section: Resultsmentioning

confidence: 64%

“Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds

Shukla

Chopra

2016

Phys. Chem. Chem. Phys.

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“…It is interesting to note that when NBO is combined with MEP analysis, the quantitative visualisation of relative charge distribution becomes easy . The charges over the pairs of atoms C21‐H26 (0.247), C22‐H27 (0.214), C52‐H57 (0.246) and C53‐H58 (0.240) confirm the electropositive character and these values are in excellent correlation with blue regions of MEP.…”

Section: Resultsmentioning

confidence: 85%

Structural Analysis, Molecular Docking and DFT Calculations of Bis(Pyrazolium Picrate) Monohydrate Interaction with Calf Thymus DNA and Microbes

et al. 2017

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Biologically evaluated Bis(Pyrazolium Picrate) Monohydrate (BPPMH) has been synthesized and crystallized by slow evaporation technique at 27 °C. Spectral and structural analyses were used to confirm the formation of the compound. The stability of BPPMH was authenticated by UV‐vis spectrophotometric method at different time intervals as well as by HOMO‐LUMO band gap analysis. Optimised geometry was used to correlate the structural confirmation of BPPMH using B3LYP/6‐311++G(d,p) level of basis set. Antimicrobial screening and its minimum inhibitory concentration has been carried out on Staphylococcus aureus and Aspergillus fumigatus. BPPMH show excellent scavenging activity against DPPH• and FRAP radicals and the antioxidant activity was validated from Fukui function calculations. DNA binding analysis confirms the hypochromism through partial intercalation via minor groove binding otherwise called as “Combilexins” and it was confirmed through emission spectral analysis. Molecular electrostatic potential analysis and Fukui functions of BPPMH indicate that there are plenty of nucleophilic, electrophilic and radical centres available for hydrogen bonding with proteins of microbes and nucleic acids of DNA. Hirshfeld surface analysis was helpful to understand inter‐ and intra‐molecular hydrogen bonding and π…π interaction between ctDNA and ligand. Molecular docking was used to identify interaction profiles, the binding energy of microbes and ctDNA. PreADMET supports QSAR of BPPMH.

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“…El análisis del potencial electrostático de la molécula de CO 2 y del grupo amino permite determinar en principio la posibilidad de formación de la interacción N … C debido a que V s (r) brinda información acerca del comportamiento reactivo de estas moléculas, 38,39 en la Figura 4 se muestran los mapas de potencial electrostático del dióxido de carbono (CO 2 ), el amoniaco (NH 3 ), la metilamina (CH 3 NH 2 ), la dimetilamina ((CH 3 ) 2 NH) y la trimetilamina ((CH 3 ) 3 N) con un valor de isosuperficie de 0.1e au -3 .…”

Section: Resultsunclassified

Estudio computacional de la interacción N⋯C en sistemas moleculares (R)nN-CO2 (n=1,2,3)

Guerra¹,

Robles²

2017

Quim. Nova

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COMPUTATIONAL STUDY OF THE INTERACTION N⋯C ON MOLECULAR SYSTEMS (R) n N-CO 2 (n=1,2,3). The structures and molecular interactions of (R) n N-CO 2 complexes of amines and CO2 in the gas phase were computationally studied by using ab-initio methods and quantum theory of atoms in molecules (QTAIM). The analysis of the electrostatic potential showed that the interaction N … C present in this type of aggregates is favored by the potential difference between the N and C atoms. On the other hand, it was observed the interaction energy is being more exergonic in molecular aggregates having highly substituted amino groups and cyclic structure; in addition, the geometric deformation of CO2 and other additional molecular interactions facilitate the process of complexation of this gas. The QTAIM analysis showed that the interaction N … C has an electrostatic character and its strength increases with the substitution of the amino group.Keywords: molecular interactions; QTAIM; exergonic; amino group; CO 2 . INTRODUCCIÓNLos problemas ambientales que han generado las emisiones de gases contaminantes a la atmosfera reciben gran atención en la actualidad debido al impacto que tienen sobre la salud humana y sobre la calidad de vida en el planeta tierra.1-3 El calentamiento global 4 es el principal problema generado por la contaminación atmosférica, el aumento descontrolado de la temperatura ligado a este fenómeno es originado por la absorción y re-emisión de radiación infrarroja por parte de los gases de efecto invernadero: vapor de agua (H 2 O), dióxido de carbono (CO 2 ) y el ozono (O 3 ). Adicionalmente, desde comienzos del siglo XIX con la revolución industrial la composición de la atmósfera se ha modificado, incrementándose la cantidad de gases de efecto invernadero. 5Uno de los gases de efecto invernadero que tiene mayor impacto sobre el aumento de la temperatura media global es el dióxido de carbono (CO 2 ), debido a que recientemente se han reportado modelos estadísticos aproximadamente lineales que relacionan las emisiones de CO 2 con el incremento anual de la temperatura en el planeta tierra basándose en su forma de emisión al compartimiento atmosférico. 6 Las fuentes de emisión de CO 2 se relacionan inequívocamente con actividades antropogénicas como la quema de combustibles fósiles, la deforestación y la actividad industrial, siendo esta última responsable del mayor porcentaje del CO 2 que es liberado al ambiente. En cuanto a la búsqueda de alternativas para reducir este fenómeno, se han establecido tratados ambientales como el protocolo de Kioto, 7 que involucran principalmente a los países industrializados y tienen como propósito disminuir y controlar las emisiones de CO 2 hasta un 5.2%, sin embargo, el cumplimiento de este tratado implica costos adicionales por parte del sector industrial, debido a que es necesario la implementación de tecnologías de captura y almacenamiento de CO 2 . 8,9 Ya que, los mecanismos de captura y almacenamiento de dióxido de carbono juegan un papel fundamental en el control de las emision...

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Electrostatic Potential Maps and Natural Bond Orbital Analysis: Visualization and Conceptualization of Reactivity in Sanger’s Reagent

Cited by 49 publications

References 50 publications

“Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds

“Pnicogen bonds” or “chalcogen bonds”: exploiting the effect of substitution on the formation of P⋯Se noncovalent bonds

Structural Analysis, Molecular Docking and DFT Calculations of Bis(Pyrazolium Picrate) Monohydrate Interaction with Calf Thymus DNA and Microbes

Estudio computacional de la interacción N⋯C en sistemas moleculares (R)nN-CO2 (n=1,2,3)

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