The quantitative estimation of the total interaction energy of a molecular system containing hydrogen bonds (H bonds) depends largely on how to identify H bonding. The conventional geometric criteria of H bonding are simple and convenient in application, but a certain amount of non-H bonding cases are also identified as H bonding. In order to investigate the wrong identification, we carry out a systematic calculation on the interaction energy of two water molecules at various orientation angles and distances using ab initio molecular dynamics method with the dispersion correction for the Becke-Lee-Yang-Parr (BLYP) functionals. It is shown that, at many orientation angles and distances, the interaction energies of the two water molecules exceed the energy criterion of the H bond, but they are still identified as H-bonded by the conventional "distance-angle" criteria. It is found that in these non-H bonding cases the wrong identification is mainly caused by short-range interaction between the two neighbouring water molecules. We thus propose that, in addition to the conventional distance and angle criteria of H bonding, the distance d(H···H) between the two neighbouring hydrogen atoms of the two water molecules should also be taken as a criterion, and the distance r(O···H) between the hydrogen atom of the H-bond donor molecule and the oxygen atom of the acceptor molecule should be restricted by a lower limit. When d(H···H) and r(O···H) are small (e.g., d(H···H) < 2.0 Å and r(O···H) < 1.62 Å), the repulsion between the two neighbouring atoms increases the total energy of the two water molecules dramatically and apparently weakens the binding of the water dimer. A statistical analysis and comparison of the numbers of the H bonds identified by using different criteria have been conducted on a Car-Parrinello ab initio molecular dynamics simulation with dispersion correction for a system of 64 water molecules at near-ambient temperature. They show that the majority of the H-bonds counted by using the conventional criteria combined with the d(H···H) criterion and the restriction of r(O···H) match what is identified by the binding energy criteria (e.g., E ≤ -10 kJ/mol), while some of them still have a binding energy that exceeds the energy criterion, indicating that the complicated quantum effects in H bonding can only be described by the three geometric parameters to a certain extent.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1063/1.4705371 | DOI Listing |
Environ Res
December 2024
State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, PR China. Electronic address:
Diffusible signal factor (DSF)-c-di-GMP-mediated strategies have been proposed as an effective regulatory approach for signal molecules in aerobic granular sludge (AGS). The increase in temperature from low to normal levels had a significant impact on AGS stability. In this study, two reactors were established to investigate the effects of different temperature rise modes (abrupt or gradual) on AGS stability.
View Article and Find Full Text PDFInt J Biol Macromol
December 2024
College of Food Science, Northeast Agricultural University, Harbin, Heilongjiang 150030, China. Electronic address:
In this study, a novel acid-induced heat-set soy protein hydrolysate (SPH) gel was successfully developed. The effects of protein (7 and 8 wt%) and glucono-δ-lactone (GDL, 4, 6, 8, and 10 wt%) concentrations on its aggregation and gelation behaviors were investigated by evaluating the structural, rheological, textural, and physical properties of the SPH gel. The structural properties revealed that GDL promoted the formation of SPH aggregates and gels, primarily via disulfide bonds and hydrophobic interactions, which were closely related to the unfolding of the protein structure, exposed hydrophobic groups, decreased protein solubility, and increased particle size and turbidity during the heating process.
View Article and Find Full Text PDFFood Chem
December 2024
School of Food Science and Engineering, and Natural Food Macromolecule Research Center, Shaanxi University of Science and Technology, Xi'an 710021, China. Electronic address:
Our previous research confirmed that resonance acoustic mixing (RAM) pretreatment effectively improved the emulsification and water retention of commercial pea protein isolate (PPI), but significantly reduced its gel performance. This study aimed to investigate the effect of transglutaminase (TGase, 0.1 %, 0.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 2024
School of Physical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, Maharashtra, India.
The dielectric behavior of Asparagine (CHNO) in water over the frequency range of 10 MHz to 30 GHz in the temperature region of 278.15-303.15 K in a step of 5 K has been carried out using time domain reflectometry (TDR) at various concentrations of asparagine.
View Article and Find Full Text PDFCell Death Discov
December 2024
Pole of Pharmacology and Therapeutics, Institut de Recherche Expérimentale et Clinique (IREC), Université catholique de Louvain (UCLouvain), Brussels, Belgium.
Hypoxic tumors are radioresistant stemming from the fact that oxygen promotes reactive oxygen species (ROS) propagation after water radiolysis and stabilizes irradiation-induced DNA damage. Therefore, an attractive strategy to radiosensitize solid tumors is to increase tumor oxygenation at the time of irradiation, ideally above a partial pressure of 10 mm-Hg at which full radiosensitization can be reached. Historically, the many attempts to increase vascular O delivery have had limited efficacy, but mathematical models predicted that inhibiting cancer cell respiration would be more effective.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!