The effective fragment potential (EFP) method is described and its capabilities illustrated using several applications. The original method, EFP1, was primarily developed to describe aqueous solvation, by representing Coulombic, induction and repulsive interactions via one-electron terms in the ab initio Hamiltonian. It is demonstrated, using water clusters, the Menshutkin reaction and the glycine neutral/ zwitterion equilibrium, that agreement with both fully ab initio calculations and experiment are excellent. More recently, the model has been extended so that it can treat any solvent, as well as more difficult links across covalent bonds. Disciplines Chemistry CommentsThis article is from Journal of Physical Chemistry A 105 (2001) The effective fragment potential (EFP) method is described and its capabilities illustrated using several applications. The original method, EFP1, was primarily developed to describe aqueous solvation, by representing Coulombic, induction and repulsive interactions via one-electron terms in the ab initio Hamiltonian. It is demonstrated, using water clusters, the Menshutkin reaction and the glycine neutral/zwitterion equilibrium, that agreement with both fully ab initio calculations and experiment are excellent. More recently, the model has been extended so that it can treat any solvent, as well as more difficult links across covalent bonds.

A new discrete/continuum solvation model has been developed by combining the effective fragment potential (EFP) for the discrete part and the polarizable continuum model (PCM) for the continuum part. The usefulness of this model is demonstrated by applying it to the calculation of the relative energies of the neutral and zwitterionic forms of glycine. These calculations were performed by treating glycine with ab initiowave functions. Water clusters were treated with bothab initio and EFP methods for comparison purposes, and the effect of the continuum was accounted for by the PCM model. The energy barrier connecting the zwitterionic and neutral three-water clusters was also examined. The computationally efficient EFP/PCM model gives results that are in close agreement with the much more expensive full ab initio/PCM calculation. The use of methods that account for electron correlation is necessary to obtain accurate relative energies for the isomers of glycine.

Water clusters (H2O)20 and (H2O)25 are explored at the Møller-Plesset second-order perturbation (MP2) level of theory. Geometry optimization is carried out on favorable structures, initially generated by the temperature basin paving (TBP) method, utilizing the fragment-based molecular tailoring approach (MTA). MTA-based stabilization energies at the complete basis set limit are accurately estimated by grafting the energy correction using a smaller basis set. For prototypical cases, the minima are established via MTA-based vibrational frequency calculations at the MP2/aug-cc-pVDZ level. The potential of MTA in tackling large clusters is further demonstrated by performing geometry optimization at MP2/aug-cc-pVDZ starting with the global minimum of (H2O)30 reported by Monte Carlo (MC) and molecular dynamics (MD) investigations. The present study brings out the efficacy of MTA in performing computationally expensive ab initio calculations with minimal off-the-shelf hardware without significant loss of accuracy.

A new solvation model that combines discrete and continuum descriptions of the solvent has been developed. The discrete solvent molecules are represented by effective fragment potentials (EFP), while the continuum is represented by the Onsager model. This (EFP+Onsager) model has been applied to the relative stabilities of the neutral and zwitterionic forms of glycine. Other supermolecule-continuum calculations were also performed, using quantum mechanical discrete waters and the isodensity polarizable continuum model (IPCM) or solvation model 5.42R (SM5.42R) for the continuum. It is shown that the Onsager model provides a poor description of the solvent in the supermolecule-continuum calculations. On the other hand, more sophisticated models can predict the correct energy order of the glycine isomers. Thus, the development of mixed methods that combine sophisticated continuum models with the discrete EFP model appear to be promising. Keywords Solvents, Polyelectrolytes Disciplines Chemistry CommentsThe A new solvation model that combines discrete and continuum descriptions of the solvent has been developed. The discrete solvent molecules are represented by effective fragment potentials ͑EFP͒, while the continuum is represented by the Onsager model. This ͑EFPϩOnsager͒ model has been applied to the relative stabilities of the neutral and zwitterionic forms of glycine. Other supermolecule-continuum calculations were also performed, using quantum mechanical discrete waters and the isodensity polarizable continuum model ͑IPCM͒ or solvation model 5.42R ͑SM5.42R͒ for the continuum. It is shown that the Onsager model provides a poor description of the solvent in the supermolecule-continuum calculations. On the other hand, more sophisticated models can predict the correct energy order of the glycine isomers. Thus, the development of mixed methods that combine sophisticated continuum models with the discrete EFP model appear to be promising.

A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.

Intramolecular cross-linking coupled with mass spectrometric identification of cross-linked amino acids is a rapid method for elucidating low-resolution protein tertiary structures or fold families. However, previous cross-linking studies on model proteins, such as cytochrome c and ribonuclease A, identified a limited number of peptide cross-links that are biased toward only a few of the potentially reactive lysine residues. Here, we report an approach to improve the diversity of intramolecular protein cross-linking starting with a systematic quantitation of the reactivity of lysine residues of a model protein, bovine cytochrome c. Relative lysine reactivities among the 18 lysine residues of cytochrome c were determined by the ratio of d0 and acetyl-d3 groups at each lysine after partial acetylation with sulfosuccinimidyl acetate followed by denaturation and quantitative acetylation of remaining unmodified lysines with acetic-d6 anhydride. These lysine reactivities were then compared with theoretically derived pKa and relative solvent accessibility surface values. To ascertain if partial N-acetylation of the most reactive lysine residues prior to cross-linking can redirect and increase the observable Lys-Lys cross-links, partially acetylated bovine cytochrome c was cross-linked with the amine-specific, bis-functional reagent, bis(sulfosuccinimidyl)suberate. After proteolysis and mass spectrometry analysis, partial acetylation was shown to significantly increase the number of observable peptides containing Lys-Lys cross-links, shifting the pattern from the most reactive lysine residues to less reactive ones. More importantly, these additional cross-linked peptides contained novel Lys-Lys cross-link information not seen in the non-acetylated protein and provided additional distance constraints that were consistent with the crystal structure and facilitated the identification of the proper protein fold.

We report a database consisting of the putative minima and ∼3.2 × 106 local minima lying within 5 kcal/mol from the putative minima for water clusters of sizes n = 3–25 using an improved version of the Monte Carlo temperature basin paving (MCTBP) global optimization procedure in conjunction with the ab initio based, flexible, polarizable Thole-Type Model (TTM2.1-F, version 2.1) interaction potential for water. Several of the low-lying structures, as well as low-lying penta-coordinated water networks obtained with the TTM2.1-F potential, were further refined at the Møller-Plesset second order perturbation (MP2)/aug-cc-pVTZ level of theory. In total, we have identified 3 138 303 networks corresponding to local minima of the clusters n = 3–25, whose Cartesian coordinates and relative energies can be obtained from the webpage https://sites.uw.edu/wdbase/. Networks containing penta-coordinated water molecules start to appear at n = 11 and, quite surprisingly, are energetically close (within 1–3 kcal/mol) to the putative minima, a fact that has been confirmed from the MP2 calculations. This large database of water cluster minima spanning quite dissimilar hydrogen bonding networks is expected to influence the development and assessment of the accuracy of interaction potentials for water as well as lower scaling electronic structure methods (such as different density functionals). Furthermore, it can also be used in conjunction with data science approaches (including but not limited to neural networks and machine and deep learning) to understand the properties of water, nature’s most important substance.

The perturbation expansion based on the locally-projected molecular orbital (LPMO PT) was applied to the study of the hydrogen-bonded networks of water clusters with up to 16 molecules. Utilizing the local nature of the occupied and excited MOs on each monomer, the charge-transfer and dispersion terms are evaluated for every pair of molecules. The two terms are strongly correlated with each other for the hydrogen-bonded pairs. The strength of the hydrogen bonds in the clusters is further classified by the types of the hydrogen donor and acceptor water molecules. The relative energies evaluated with the LPMO PT among the isomers of (H2O)6, (H2O)11, and (H2O)16 agree very well with those obtained from CCSD(T) calculations with large basis sets. The binding energy of the LPMO PT is approximately free of the basis set superposition errors caused both by the orbital basis inconsistency and by the configuration basis inconsistency.