Evaluation of the criteria of hydrogen bonding in highly associated liquids

Swiatla-Wojcik, Dorota

doi:10.1016/j.chemphys.2007.10.009

Cited by 66 publications

(72 citation statements)

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“…It is known that the strength of the hydrogen bonds depends, under the geometric criteria, on acceptor-hydrogen distances as short as possible (for very strong bonds, the distance can be even shorter than 2 Å), and donor-hydrogen-acceptor angles as close to 180° as possible. 54,55 Table 1 shows the results for the main conformers of each analog. For 12a , the most stable geometry shows a strong “1,3-diaxial” hydrogen bond between an axial O-H and an axial O bonded to different P atoms (d H-O = 1.82 Å), and a very strong hydrogen bond between the other acidic hydrogen (equatorial) and the nearby nitrogen atom (d H-N = 1.68 Å), which fixes the conformation of the side chain (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

New insights into molecular recognition of 1,1-bisphosphonic acids by farnesyl diphosphate synthase

Ferrer‐Casal

Galizzi

et al. 2014

Bioorganic & Medicinal Chemistry

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As part of our project pointed at the search of new antiparasitic agents against American trypanosomiasis (Chagas disease) and toxoplasmosis a series of 2-alkylaminoethyl-1-hydroxy-1,1-bishosphonic acids has been designed, synthesized and biologically evaluated against the etiologic agents of these parasitic diseases, Trypanosoma cruzi and Toxoplasma gondii, respectively, and also towards their target enzymes, T. cruzi and T. gondii farnesyl pyrophosphate synthase (FPPS), respectively. Surprisingly, while most pharmacologically active bisphosphonates have a hydroxyl group at the C-1 position, the additional presence of an amino group at C-3 resulted in decreased activity towards either T. cruzi cells or TcFPPS. Density functional theory calculations justify this unexpected behavior. Although these compounds were devoid of activity against T. cruzi cells and TcFPPS, they were efficient growth inhibitors of tachyzoites of T. gondii. This activity was associated with a potent inhibition of the enzymatic activity of TgFPPS. Compound 28 arises as a main example of this family of compounds exhibiting an ED50 value of 4.7 μM against tachyzoites of T. gondii and an IC50 of 0.051 μM against TgFPPS.

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Section: Resultsmentioning

confidence: 99%

New insights into molecular recognition of 1,1-bisphosphonic acids by farnesyl diphosphate synthase

Ferrer‐Casal

Galizzi

et al. 2014

Bioorganic & Medicinal Chemistry

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“…Within the frame work of computer simulation, special criteria are used to identify hydrogen bonded molecules [26]. In gen eral, they are divided into two types: energetic and geo metric criteria [27]. In the first case, molecules are considered to be hydrogen bonded, provided that the pair intermolecular interaction energy is lower than some threshold value.…”

Section: Resultsmentioning

confidence: 99%

Dynamics of a network of hydrogen bonds upon water electrocrystallization

Khusnutdinoff

2013

Colloid J

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Computer simulation is employed to study the dynamics of a network of hydrogen bonds and the structural properties of water placed between graphene layers. The presence of the graphene walls has been shown to substantially affect the water phase diagram. Glass transition processes are observed in the system, and liquid water completely passes to an amorphous state. Moreover, it has been established that the imposi tion of an external electric field with strength E ≥ 0.5 V/Å on the system subjected to increased pressure results in structural ordering of water. It has been found that water located between graphene layers is transformed into Ic cubic ice. The electrocrystallization of water has been shown to substantially change the dynamics of the network of hydrogen bonds.

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“…The hybrid energy-distance criterion [4] was shown to overestimate the size of hydrogen-bonded clusters in conditions of high temperature and low density [7]. The H-bond energy threshold E c has been taken from the statistical distributions of the pair interaction energy c .…”

Section: Computational Detailsmentioning

confidence: 99%

“…The H-bond criterion used in the investigation of the thermodynamic conditions involves the interaction energy E, the distance between the hydrogen atom of H-donor and the oxygen atom of H-acceptor r O…H , and the angle between the OH bond of the H-donor and the line connecting the oxygen atoms of two molecules α O…H-O [7]:…”

Section: Computational Detailsmentioning

confidence: 99%

“…The other two points, TS4 and TS5, are in the supercritical region and represent dense and low-density fluid, respectively. A quantification of hydrogen-bonded pairs has been performed using the recently proposed extended energetic criterion, which takes account of the intermolecular interaction and separation, and the orientation of H-donating molecule [7].…”

Section: Introductionmentioning

confidence: 99%

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