From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach.

Accurately characterizing molecular interactions stands as a pivotal requirement for ensuring the reliability of molecular dynamics simulations. In line with our bond-dipole-based interaction model proposed by Gao et al. [X.-C. Gao, Q. Hao and C.-S. Wang, J. Chem. Theory Comput., 2017, 13, 2730-2741.], we have implemented an efficient and concise approach to compute electrostatic potential. This methodology capitalizes on the polarizable nature of chemical bond dipoles, resulting in a model of remarkable simplicity. In this study, we have revised the polarizable bond-dipole-based force field (PBFF) through the meticulous curation of quantum chemical data sets. These data sets encompass a comprehensive collection of 40 000 conformations, including those of water, methylamine, methanol, and N-methylacetamide. Additionally, we incorporate 520 hydrogen-bonded dimers into our data sets. In pursuit of enhanced accuracy in molecular dynamics simulations and a more faithful representation of potential energy landscapes, we undertook the re-optimization of the nonbonded parameters within the PBFF framework. Concurrently, we intricately fine-tuned the bonded parameters. The results of our comprehensive evaluation denote that this newly optimized force field method adeptly and efficiently computes structural characteristics, harmonic frequencies, and interaction energies. Overall, this study provides further validation for the applicability of PBFF in molecular dynamics simulations.

Serum iron levels are an independent predictor of in-hospital mortality of critically ill patients: a retrospective, single-institution study.

OBJECTIVE: This study aimed to examine the relationship between serum iron levels and in-hospital mortality in critically ill patients. METHODS: We retrospectively studied 250 critically ill patients who received treatment at the intensive care unit between June 2015 and May 2017. Blood chemistry and hepatic and renal function were measured. Kaplan-Meier survival curves were plotted according to serum iron levels. Correlations between serum iron levels and other variables were analyzed. RESULTS: A total of 165 (66.0%) patients had abnormally low serum iron levels (<10.6 µmol/L). Patients who died during hospitalization had markedly higher Acute Physiology and Chronic Health Evaluation II scores and significantly lower serum iron levels compared with those who survived. Cumulative survival was significantly lower in patients with low serum iron levels than in those with normal serum iron levels in subgroup analysis of older patients (n = 192). Multivariate regression analysis showed that, after adjusting for relevant factors, low serum iron levels remained an independent risk for in-hospital mortality (odds ratio 2.014; 95% confidence interval 1.089, 3.725). CONCLUSIONS: Low serum iron levels are present in a significant proportion of critically ill patients and are associated with higher in-hospital mortality, particularly in older patients.

Temperature-Responsive Chiral (A)6B Supramolecular Cages Based on Conformational Preferences.

Two chiral (A)6B-typed supramolecular cages were constructed from hydrogen-bonded C6 -symmetric zinc porphyrin hexamers and chiral C3-symmetric pyridyl hexadentates with a core of 1,3,5-triphenylbenzene. Circular dichroism and molecular simulations revealed that the symmetry of the supramolecular cages switched from pseudo-C3v to C3 with the rotational confinement of the biphenyl backbones at low temperatures, which generated conformationally chiral transfer and amplification. This unique phenomenon suggests a new strategy to develop smart materials with high sensitivity and excellent reversibility.

Rapid evaluation of the binding energies in hydrogen-bonded amide-thymine and amide-uracil dimers in gas phase.

The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 48 hydrogen-bonded amide-thymine and amide-uracil dimers are evaluated from the analytic potential energy function established in our lab recently. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6-311+G** calculations by including the BSSE correction. For all the 48 dimers, the analytic potential energy function yields the binding energies of the MP2/6-311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 46 dimers, only two differences are larger than 0.50 kcal/mol and the largest one is only 0.60 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6-311+G** with BSSE correction within the error limits of 0.050 Å for all the 48 dimers. The analytic potential energy function is further applied to four more complicated hydrogen-bonded amide-base systems involving amino acid side chain and ß-sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen-bonded amide-base dimers quickly and accurately.

A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides, acetamides, and N-methylformamides.

A scheme is proposed in this article to predict the cooperativity in hydrogen bond chains of formamides, acetamides, and N-methylformamides. The parameters needed in the scheme are derived from fitting to the hydrogen bonding energies of MP2/6-31+G** with basis set superposition error (BSSE) correction of the hydrogen bond chains of formamides containing from two to eight monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in the chains of formamides containing 9 and 12 monomeric units, in the chains of acetamides containing from two to seven monomeric units, in the chains of N-methylformamides containing from two to seven monomeric units. The calculation results show that the cooperativity predicted by the scheme proposed in this paper is in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, demonstrating that the scheme proposed in this article is reasonable. Based on our scheme, a cooperativity effect of almost 240% of the dimer hydrogen bonding energy in long hydrogen bond formamide chains, a cooperativity effect of almost 190% of the dimer hydrogen bonding energy in long hydrogen bond acetamide chains, and a cooperativity effect of almost 210% of the dimer hydrogen bonding energy in long hydrogen bond N-methylformamide chains are predicted. The scheme is further applied to some heterogeneous chains containing formamide, acetamide, and N-methylformamide. The individual hydrogen bonding energies in these heterogeneous chains predicted by our scheme are also in good agreement with those obtained from Møller-Plesset calculations including BSSE correction.

Rapid prediction of the hydrogen bond cooperativity in N-methylacetamide chains.

A method is proposed to rapidly predict the hydrogen bond cooperativity in N-methylacetamide chains. The parameters needed are obtained from the fittings to the hydrogen bonding energies in the formamide chains containing 2 to 8 monomeric units. The scheme is then used to calculate the individual hydrogen bonding energies in N-methylacetamide chains containing 2 to 7 monomeric units. The cooperativity predicted is in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction. Our scheme is further employed to predict the individual hydrogen bonding energies in larger N-methylacetamide chains containing up to 200 monomeric N-methylacetamide units, to which the MP2 method cannot be applied. Based on our scheme, a cooperative effect of over 170% of the dimer hydrogen bonding energy in long N-methylacetamide chains is predicted. The method is also applied to heterogeneous chains containing formamide, acetamide, N-methylformamide, and N-methylacetamide. The individual hydrogen bonding energies in these heterogeneous chains are also in good agreement with those obtained from MP2 calculations with the BSSE correction, further demonstrating that our method is reasonable.

An analytic potential energy function for the amide-amide and amide-water intermolecular hydrogen bonds in peptides.

An analytic potential energy function is proposed and applied to evaluate the amide-amide and amide-water hydrogen-bonding interaction energies in peptides. The parameters in the analytic function are derived from fitting to the potential energy curves of 10 hydrogen-bonded training dimers. The analytic potential energy function is then employed to calculate the N-H...O=C, C-H...O=C, N-H...OH2, and C=O...HOH hydrogen-bonding interaction energies in amide-amide and amide-water dimers containing N-methylacetamide, acetamide, glycine dipeptide, alanine dipeptide, N-methylformamide, N-methylpropanamide, N-ethylacetamide and/or water molecules. The potential energy curves of these systems are therefore obtained, including the equilibrium hydrogen bond distances R(O...H) and the hydrogen-bonding energies. The function is also applied to calculate the binding energies in models of beta-sheets. The calculation results show that the potential energy curves obtained from the analytic function are in good agreement with those obtained from MP2/6-31+G** calculations by including the BSSE correction, which demonstrate that the analytic function proposed in this work can be used to predict the hydrogen-bonding interaction energies in peptides quickly and accurately.