Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space

The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides a thorough sampling of an extended chemical space, while the D442×10 set features dissociation curves for selected complexes. In total, they provide 5,178 new CCSD(T)/CBS data points of the highest quality. The new data have been combined with previous NCIA data sets in a comprehensive test of dispersion-corrected DFT methods, identifying the ones that achieve high accuracy in all types of non-covalent interactions in a broad chemical space. Additional tests of dispersion-corrected MP2 and semiempirical QM methods are also reported.

Initial Decomposition Mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under Shock Loading: ReaxFF Parameterization and Molecular Dynamic Study

We report a reactive molecular dynamic (ReaxFF-MD) study using the newly parameterized ReaxFF-lg reactive force field to explore the initial decomposition mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under shock loading (shock velocity >6 km/s). The new ReaxFF-lg parameters were trained from massive quantum mechanics data and experimental values, especially including the bond dissociation curves, valence angle bending curves, dihedral angle torsion curves, and unimolecular decomposition paths of 3-Nitro-1,2,4-triazol-5-one (NTO), 1,3,5-Trinitro-1,3,5-triazine (RDX), and 1,1-Diamino-2,2-dinitroethylene (FOX-7). The simulation results were obtained by analyzing the ReaxFF dynamic trajectories, which predicted the most frequent chain reactions that occurred before NTO decomposition was the unimolecular NTO merged into clusters ((C2H2O3N4)n). Then, the NTO dissociated from (C2H2O3N4)n and started to decompose. In addition, the paths of NO2 elimination and skeleton heterocycle cleavage were considered as the dominant initial decomposition mechanisms of NTO. A small amount of NTO dissociation was triggered by the intermolecular hydrogen transfer, instead of the intramolecular one. For α-NTO, the calculated equation of state was in excellent agreement with the experimental data. Moreover, the discontinuity slope of the shock-particle velocity equation was presented at a shock velocity of 4 km/s. However, the slope of the shock-particle velocity equation for β-NTO showed no discontinuity in the shock wave velocity range of 3–11 km/s. These studies showed that MD by using a suitable ReaxFF-lg parameter set, could provided detailed atomistic information to explain the shock-induced complex reaction mechanisms of energetic materials. With the ReaxFF-MD coupling MSST method and a cheap computational cost, one could also obtain the deformation behaviors and equation of states for energetic materials under conditions of extreme pressure.

Treatment of sickle cell disease by increasing oxygen affinity of hemoglobin

The issue of treating sickle cell disease with drugs that increase hemoglobin oxygen affinity has come to the fore with the FDA approval in 2019 of voxelotor, the only anti-sickling drug approved since hydroxyurea in 1998. Voxelotor reduces sickling by increasing the concentration of the non-polymerizing, high oxygen affinity R (oxy) conformation of HbS. Treatment of sickle cell patients with voxelotor increases Hb levels and decreases indicators of hemolysis, but with no indication as yet that it reduces the frequency of pain episodes. Here we use the allosteric model of Monod, Wyman, and Changeux to simulate whole blood oxygen dissociation curves and red cell sickling in the absence and presence of voxelotor under the in vivo conditions of rapid oxygen pressure decreases. Our modeling agrees with experiments using a new robust assay, which shows the very large, expected decrease in sickling from the drug. The modeling indicates, however, that the increase in oxygen delivery from reduced sickling is largely offset by the increase in oxygen affinity. The net result is that the drug increases overall oxygen delivery only at the very lowest oxygen pressures. Reduction of sickling does, however, mitigate against red cell damage and explains the observed decrease in hemolysis. More importantly, our modeling of in vivo oxygen dissociation, sickling, and oxygen delivery suggests that drugs that increase fetal hemoglobin or decrease MCHC, should be more therapeutically effective than drugs that increase oxygen affinity.

Red Blood Cell 2,3-Diphosphoglycerate Decreases in Response to a 30 km Time Trial Under Hypoxia in Cyclists

Red blood cell 2,3-diphosphoglycerate (2,3-DPG) is one of the factors of rightward-shifted oxygen dissociation curves and decrease of Hb-O2 affinity. The reduction of Hb-O2 affinity is beneficial to O2 unloading at the tissue level. In the current literature, there are no studies about the changes in 2,3-DPG level following acute exercise in moderate hypoxia in athletes. For this reason, the aim of this study was to analyze the effect of prolonged intense exercise under normoxic and hypoxic conditions on 2,3-DPG level in cyclists. Fourteen male trained cyclists performed a simulation of a 30 km time trial (TT) in normoxia and normobaric hypoxia (FiO2 = 16.5%, ~2,000 m). During the TT, the following variables were measured: power, blood oxygen saturation (SpO2), and heart rate (HR). Before and immediately after exercise, the blood level of 2,3-DPG and acid–base equilibrium were determined. The results showed that the mean SpO2 during TT in hypoxia was 8% lower than in normoxia. The reduction of SpO2 in hypoxia resulted in a decrease of average power by 9.6% (p < 0.001) and an increase in the 30 km TT completion time by 3.8% (p < 0.01) compared to normoxia. The exercise in hypoxia caused a significant (p < 0.001) decrease in 2,3-DPG level by 17.6%. After exercise in normoxia, a downward trend of 2,3-DPG level was also observed, but this effect was not statistically significant. The analysis also revealed that changes of acid–base balance were significantly larger (p < 0.05) after exercise in hypoxia than in normoxia. In conclusion, intense exercise in hypoxic conditions leads to a decrease in 2,3-DPG concentration, primarily due to exercise-induced acidosis.

Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation

Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

Variational Quantum Chemistry Programs in JaqalPaq

We present example quantum chemistry programs written with JaqalPaq, a python meta-programming language used to code in Jaqal (Just Another Quantum Assembly Language). These JaqalPaq algorithms are intended to be run on the Quantum Scientific Computing Open User Testbed (QSCOUT) platform at Sandia National Laboratories. Our exemplars use the variational quantum eigensolver (VQE) quantum algorithm to compute the ground state energies of the H2, HeH+, and LiH molecules. Since the exemplars focus on how to program in JaqalPaq, the calculations of the second-quantized Hamiltonians are performed with the PySCF python package, and the mappings of the fermions to qubits are obtained from the OpenFermion python package. Using the emulator functionality of JaqalPaq, we emulate how these exemplars would be executed on an error-free QSCOUT platform and compare the emulated computation of the bond-dissociation curves for these molecules with their exact forms within the relevant basis.

LILBID laser dissociation curves: a mass spectrometry-based method for the quantitative assessment of dsDNA binding affinities

One current goal in native mass spectrometry is the assignment of binding affinities to noncovalent complexes. Here we introduce a novel implementation of the existing laser-induced liquid bead ion desorption (LILBID) mass spectrometry method: this new method, LILBID laser dissociation curves, assesses binding strengths quantitatively. In all LILBID applications, aqueous sample droplets are irradiated by 3 µm laser pulses. Variation of the laser energy transferred to the droplet during desorption affects the degree of complex dissociation. In LILBID laser dissociation curves, laser energy transfer is purposely varied, and a binding affinity is calculated from the resulting complex dissociation. A series of dsDNAs with different binding affinities was assessed using LILBID laser dissociation curves. The binding affinity results from the LILBID laser dissociation curves strongly correlated with the melting temperatures from UV melting curves and with dissociation constants from isothermal titration calorimetry, standard solution phase methods. LILBID laser dissociation curve data also showed good reproducibility and successfully predicted the melting temperatures and dissociation constants of three DNA sequences. LILBID laser dissociation curves are a promising native mass spectrometry binding affinity method, with reduced time and sample consumption compared to melting curves or titrations.

A broad diversity in oxygen affinity to haemoglobin

Oxygen affinity to haemoglobin is indicated by the p50 value (pO2 at 50% O2Hb) and critically determines cellular oxygen availability. Although high Hb-O2 affinity can cause tissue hypoxia under conditions of well O2 saturated blood, individual differences in p50 are commonly not considered in clinical routine. Here, we investigated the diversity in Hb-O2 affinity in the context of physiological relevance. Oxyhaemoglobin dissociation curves (ODCs) of 60 volunteers (18–40 years, both sexes, either endurance trained or untrained) were measured at rest and after maximum exercise (VO2max) test. At rest, p50 values of all participants ranged over 7 mmHg. For comparison, right shift of ODC after VO2max test, representing the maximal physiological range to release oxygen to the tissue, indicated a p50 difference of up to 10 mmHg. P50 at rest differs significantly between women and men, with women showing lower Hb-O2 affinity that is determined by higher 2,3-BPG and BPGM levels. Regular endurance exercise did not alter baseline Hb-O2 affinity. Thus, p50 diversity is already high at baseline level and needs to be considered under conditions of impaired tissue oxygenation. For fast prediction of Hb-O2 affinity by blood gas analysis, only venous but not capillary blood samples can be recommended.

No evidence of hemoglobin damage by SARS-CoV-2 infection

SARS-CoV-2 disease (COVID-19) has affected over 22 million patients worldwide as of August 2020. As the medical community seeks better understanding of the underlying pathophysiology of COVID-19, several theories have been proposed. One widely shared theory suggests that SARS-CoV-2 proteins directly interact with human hemoglobin (Hb) and facilitate removal of iron from the heme prosthetic group, leading to the loss of functional hemoglobin and accumulation of iron. Herein, we refute this theory. We compared clinical data from 21 critically ill COVID-19 patients to 21 non-COVID-19 ARDS patient controls, generating hemoglobin-oxygen dissociation curves from venous blood gases. This curve generated from the COVID-19 cohort matched the idealized oxygen-hemoglobin dissociation curve well (Pearson correlation, R2 = 0.97, P<0.0001; CV(RMSD) = 7.3%). We further analyzed hemoglobin, total bilirubin, lactate dehydrogenase, iron, ferritin, and haptoglobin levels. For all analyzed parameters, patients with COVID-19 had similar levels compared to patients with ARDS without COVID-19. These results indicate that patients with COVID-19 do not exhibit any hemolytic anemia or a shift in the normal hemoglobin-oxygen dissociation curve. We therefore conclude that COVID-19 does not impact oxygen delivery through a mechanism involving red cell hemolysis and subsequent removal of iron from the heme prosthetic group in hemoglobin.