Junming Ho

Bio: Junming Ho is an academic researcher from University of New South Wales. The author has contributed to research in topics: Solvation & Solvent models. The author has an hindex of 24, co-authored 79 publications receiving 2622 citations. Previous affiliations of Junming Ho include Institute of High Performance Computing Singapore & Australian National University.

A universal approach for continuum solvent pK a calculations: are we there yet?

Abstract: This paper reviews several pKa calculation strategies that are commonly used in aqueous acidity predictions. Among those investigated were the direct or absolute method, the proton exchange scheme, and the hybrid cluster–continuum (Pliego and Riveros) and implicit–explicit (Kelly, Cramer and Truhlar) models. Additionally, these protocols are applied in the pKa calculation of 55 neutral organic and inorganic acids in conjunction with various solvent models, including the CPCM-UAKS/UAHF, IPCM, SM6 and COSMO-RS, with a view to identifying a universal approach for accurate pKa predictions. The results indicate that the direct method is unsuitable for general pKa calculations, although moderately accurate results (MAD <3 units) are possible for certain classes of acids, depending on the choice of solvent model. The proton exchange scheme generally delivers good results (MAD <2 units), with CPCM-UAKS giving the best performance. Furthermore, the sensitivity of this approach to the choice of reference acid can be substantially lessened if the solvation energies for ionic species are calculated via the IPCM cluster–continuum approach. Reference-independent hybrid approaches that include explicit water molecules can potentially give reasonably accurate values (MAD generally ~2 units) depending on the solvent model and the number of explicit water molecules added.

Comment on the correct use of continuum solvent models.

Abstract: The development of dielectric continuum solvent models 1,2 (CSMs) has facilitated the study of chemical reactions in the condensed phase in a computationally efficient manner. These methods have been parametrized to deliver accurate values of the free energies of solvation. which can be added to accurate values of the free energies in the gas-phase, to obtain the corresponding solution-phase free energy: G soln = G gas + ΔG solv + RTln(RT/P) (1) where the final term converts from the gas-phase standard state (defined by T and P) to the solution-phase standard state of 1 M. However, there are a growing number of recent studies that employ alternative approaches to evaluating G soln . This comment aims to highlight some of their shortcomings as well as clarify some potential points of confusion concerning the usage of these models.

Computational electrochemistry: prediction of liquid-phase reduction potentials

Abstract: This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car–Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Are thermodynamic cycles necessary for continuum solvent calculation of pKas and reduction potentials

Abstract: Continuum solvent calculations of pKas and reduction potentials usually entail the use of a thermodynamic cycle to express the reaction free energy in terms of gas phase energies and free energies of solvation. In this work, we present a systematic study comparing the solution phase free energy changes obtained in this manner with those directly computed within the SMD solvation model against a large test set of 117 pKas and 42 reduction potentials in water and DMSO. The inclusion of vibrational contributions in the free energy of solvation has a negligible impact on the accuracy of thermodynamic cycle predictions of pKas and reduction potentials. Additionally, when gas phase energies in the thermodynamic cycle are computed at more accurate levels of theory, very similar results (mean unsigned difference of 0.5 kcal mol−1) can be achieved when the high-level computations (MP2/GTMP2Large and G3(MP2)-RAD(+)) are directly carried out within the continuum model. Increasing the accuracy of the electronic structure theory may or may not improve the agreement with experiment suggesting that the error is largely in the solvation model. For amino acids where their gas and solution phase species exist as different tautomers, the direct approach provided a significant improvement in calculated pKas. These results demonstrate that direct calculation of solution phase pKas and reduction potentials within the SMD model provides a general and reliable approximation to corresponding thermodynamic cycle based protocols, and is recommended for systems where solvation induced changes in geometry are significant. Further studies are necessary to ascertain whether the results are generalisable to other continuum solvation models.

Calculating Free Energy Changes in Continuum Solvation Models.

Abstract: We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [Phys. Chem. Chem. Phys. 2015, 17, 2859]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar—the mean errors for Gibbs free energy changes of neutral and ionic reactions are a...

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation

Abstract: We find that vibrational contributions to a solute’s free energy are in general insensitive to whether the solute vibrational frequencies are computed in the gas phase or in solution. In most cases, the difference is smaller than the intrinsic error in solvation free energies associated with the continuum approximation to solvation modeling, although care must be taken to avoid spurious results associated with limitations in the quantum-mechanical harmonic-oscillator approximation for very low-frequency molecular vibrations. We compute solute vibrational partition functions in aqueous and carbon tetrachloride solution and compare them to gas-phase molecular partition functions computed with the same level of theory and the same quasiharmonic approximation for the diverse and extensive set of molecules and ions included in the training set of the SMD continuum solvation model, and we find mean unsigned differences in vibrational contributions to the solute free energy of only about 0.2 kcal/mol. On the bas...

Homogeneously Catalyzed Electroreduction of Carbon Dioxide-Methods, Mechanisms, and Catalysts

Abstract: The utilization of CO2 via electrochemical reduction constitutes a promising approach toward production of value-added chemicals or fuels using intermittent renewable energy sources. For this purpose, molecular electrocatalysts are frequently studied and the recent progress both in tuning of the catalytic properties and in mechanistic understanding is truly remarkable. While in earlier years research efforts were focused on complexes with rare metal centers such as Re, Ru, and Pd, the focus has recently shifted toward earth-abundant transition metals such as Mn, Fe, Co, and Ni. By application of appropriate ligands, these metals have been rendered more than competitive for CO2 reduction compared to the heavier homologues. In addition, the important roles of the second and outer coordination spheres in the catalytic processes have become apparent, and metal–ligand cooperativity has recently become a well-established tool for further tuning of the catalytic behavior. Surprising advances have also been made ...