Theoretical investigation of hydrogen bonding in Watson–Crick, Hoogestein and their reversed and other models: comparison and analysis for configurations of adenine–thymine base pairs in 9 models

Monajjemi, Majid; Chahkandi, Behzad

doi:10.1016/j.theochem.2004.09.048

Cited by 39 publications

(21 citation statements)

References 47 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is true even when considering only the hydrogen bonds that are possible within the (T 20 ϩ XH) Ϫ3 complexes. According to the most recent DFT calculations, the A-T interaction energy may be as large as 17 kcal mol Ϫ1 [38]. Based on the similarity between the theoretical A-T interaction energy value and the experimental dissociation E a for the (T 20 ϩ AH) Ϫ3 complex, ϳ20 kcal mol Ϫ1 , the possibility of neutral A-T interactions in the (T 20 ϩ AH) Ϫ3 complex cannot be ruled out.…”

Section: Bird Of Noncovalent (T 20 ϩ Xh) ϫ3 Complexesmentioning

confidence: 99%

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

Daneshfar

Klassen

2006

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).

show abstract

Section: Bird Of Noncovalent (T 20 ϩ Xh) ϫ3 Complexesmentioning

confidence: 99%

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

Daneshfar

Klassen

2006

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…In the all calculations molecule were treated with 6-31G* basis set, carried out by B3LYP function 67,68 . All these cases have been taken into account for several parameters such as energy,dipole moment, quadrupole moment, energy gap, electron energy and etc [69][70][71] .…”

Section: Methods and Calculationsmentioning

confidence: 99%

Anti-cancer properties of green Tea Probed viaquantum mechanics calculations

Chitsazan¹

2015

Orient. J. Chem

View full text Add to dashboard Cite

Tea, from the plant camellia sinensis, is consumed in different parts of the world as green, black or oolong tea. Among all of these, however, the most significant effects on human health have been observed with the consumption of green tea. Green tea contains polyphenols, which include flavanols, flavandiols, flavonoids, and phenolic acids. Most of the green tea polyphenols (GTPs) are flavonols, commonly known as catechins. There are four kinds of catechins mainly find in green tea: epicatechin, epigallocatechin, epicatechin-3-gallate, and EGCG. Green tea catechins have demonstrated significant antioxidant, anticarcinogenic, anti-inflammatory, thermogenic, probiotic, and antimicrobial properties in numerous human, animal, and in vitro studies. In the present study, four type catechins of green tea were studied. For each catechin ab initio method was employed for calculations and related parameters were computed.

show abstract

“…Based on our calculations especially various B n N n Rings, Benzene and naphthalene, (k) is mostly positive [31][32][33][34][35][36][37][38][39][40] , and the negative values are belong to some critical or boundary points. In the case of an axially symmetric tensor, s 22 equals either s 11 or s 33 and k= ±1 therefore a = W/3, and the parameter "a" and "k" are zero when s 22 = s iso and the parameter "m" used with the Herzfeld-Berger is related to the span of a tensor.…”

Section: Theoretical Background Nmr Shieldingmentioning

confidence: 99%

A study of Fe3O4@ Si18O27 catalyst through Statistical-Nucleus Independent Chemical Shifts(S-NICS) method

Soofi¹,

Monajjemi²

2016

Orient. J. Chem

Self Cite

View full text Add to dashboard Cite

There are no theoretical or mathematical reports of a statistical approach in NMR shielding and nucleus independent chemical shifts, while the asymmetry (η) and skew (κ) parameters are fluctuated in short distances and are alternative in long distances. In the case of axially symmetric tensor, σ 22 equals either σ 11 or σ 33 , skew is κ= ±1 and by changing asymmetry between 0 ≤ η ≤ +1 skew will be changed between -1 ≤ κ ≤ +1 , meanwhile the parameter "κ" is zero when σ 22 = σ iso . In this work, we have investigated a statistical method by computing of Nucleus-Independent Chemical Shifts (S-NICS) in point of probes motions in a sphere of shielding and deshielding spaces of SiO 2 rings. Monajjemi in the previous work 24 , has investigated a new method as the name " S-NICS" which this method is suitable for calculation the aromaticity in the non-benzene rings such as SiO 2 rings which is a famous catalyst for organic chemical synthesize and reaction. Although S-NICS values for some molecules such as benzene, borazine and naphthalene can be indicated as the aromaticity criterion, for other cases such as B n N n H x and their hydrogenated derivatives, these values indicate electromagnetic index. Finally, we have introduced a schematic diagram of statisticalnucleus independent chemical shifts for ab-initio calculations in Gaussian program, Games or other software.

show abstract

Theoretical investigation of hydrogen bonding in Watson–Crick, Hoogestein and their reversed and other models: comparison and analysis for configurations of adenine–thymine base pairs in 9 models

Cited by 39 publications

References 47 publications

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

Anti-cancer properties of green Tea Probed viaquantum mechanics calculations

A study of Fe3O4@ Si18O27 catalyst through Statistical-Nucleus Independent Chemical Shifts(S-NICS) method

Contact Info

Product

Resources

About