A relativistic coupled-cluster interaction potential and rovibrational constants for the xenon dimer

An efficient method to predict protein thermostability in alanine mutation

The relationship between protein sequence and its thermodynamic stability is a critical aspect of computational protein design. In this work, we present a new theoretical method to calculate the free energy change (ΔΔG) resulting from a single-point amino acid mutation to alanine in a protein sequence. The method is derived based on physical interactions and is very efficient in estimating the free energy changes caused by a series of alanine mutations from just a single molecular dynamics (MD) trajectory. Numerical calculations are carried out on a total of 547 alanine mutations in 19 diverse proteins whose experimental results are available. The comparison between the experimental ΔΔG_exp and the calculated values shows a generally good correlation with a correlation coefficient of 0.67. Both the advantages and limitations of this method are discussed. This method provides an efficient and valuable tool for protein design and engineering.

More about properties of Morse oscillator

Using Birge-Sponer extrapolation we have analyzed the approximation of the potential of a real diatomic molecule by the Morse model, which implies a constant value of anharmonicity ωx. The real values of ωx*(v) for each vibrational level are estimated from transition frequencies between neighboring levels. The dependence of ωx* on the vibrational quantum number v up to dissociation is calculated from the literature data for the ground electronic state of H₂, O₂, Be₂, Li₂, ArXe, Xe₂, Kr₂ and the excited state of Li₂. Characteristic features of deviations of the anharmonicity parameter x* - x from the Morse model are described.

Accurate elemental boiling points from first principles

The normal boiling point (NBP) is a fundamental property of liquids and marks the intersection of the Gibbs energies of the liquid and the gas-phase at ambient pressure. This work provides the first comprehensive demonstration of the calculation of boiling points of atomic liquids through first-principles molecular-dynamics simulations. To this end, thermodynamic integration (TDI) and perturbation theory (TPT) are combined with a density-functional theory (DFT) Hamiltonian, which provides absolute Gibbs energies, internal energies, and entropies of atomic liquids with an accuracy of a few meV/atom. Linear extrapolation to the intersection with the Gibbs energy of a non-interacting gas-phase eventually pins-down the NBPs. While these direct results can already be quite accurate, they are susceptible to a systematic over or underbinding of the employed density functional. It is shown how this dependency can be strongly reduced and the robustness of the method increased through a simple linear correction termed λ-scaling. Eventually, by carefully tuning of the technical parameters of the approach, the walltime per element is reduced from weeks to about a day (10-20k core-hours), enabling extensive testing for B, Al, Na, K, Ca, Sr, Ba, Mn, Cu, Xe, and Hg. This comprehensive benchmark demonstrates the excellent performance and robustness of the approach with a mean absolute deviation (MAD) of less than 2% from experimental NBPs and very similar accuracy for liquid entropies (MAD 2.3 J (mol K)-1, 2% relative). In some cases, the uncertainties in the predictions are several times smaller than the variation between literature values, allowing us to clear out long-standing ambiguities in the NBPs of B and Ba.

Ab initio relativistic potential energy surfaces of benzene-Xe complex with application to intermolecular vibrations

The benzene-Xe (BXe) complex in its electronic ground state is studied using ab initio methods. Since this complex contains the heavy Xe atom, the relativistic effects cannot be neglected. We test two different approaches that describe the scalar relativistic effects in the framework of the coupled-cluster level of theory with single, double, and perturbative triple excitations, used for the interaction energy calculations. The first one is based on the small core pseudopotential (PP), and the second one is based on the explicit treatment of scalar relativistic effects using the Douglas-Kroll-Hess (DKH) Hamiltonian. A few basis sets are tested with the PP and DKH, and for each one, the analytical potential energy surface (PES) is constructed. It is shown that the difference between PESs determined with PP and DKH methods is small, if the orbitals of the 4d subshell in Xe are correlated. We select the most appropriate approach for the calculation of the potential energy surface of BXe, with respect to accuracy and computational cost. The optimal level of theory includes a small Dunning's basis set for the benzene monomer and a larger PP basis set for Xe supplemented by midbond functions. The PES obtained using such an approach provides a reasonable accuracy when compared to the empirical one derived from the microwave spectra of BXe. The empirical and the theoretical values of intermolecular vibrational energies agree within 0.5 cm^-1 up to second overtones. The vibrational energy level pattern of BXe is characterized by a distinct polyad structure.

Transverse migration and microfluidic concentration of DNA using Newtonian buffers

We present experimental evidence that DNA can be concentrated due to an electrohydrodynamic coupling between a pressure-driven flow and a parallel electric field. The effects of buffer properties on the process were measured in a microfluidic channel. The concentration rates and the efficiency of trapping DNA were quantified as functions of the ion and polymer concentrations of the buffer solution. Buffers with large ion concentrations hindered the ability to trap DNA, reducing the short-time efficiency of the concentration process from nearly 100% to zero. Importantly, DNA was trapped in the microfluidic channel even when the buffer solution lacked any measurable viscoelastic response. These observations indicate that electrohydrodynamic migration drives the concentration of DNA. We found no evidence of viscoelastic migration in these experiments.

From sticky-hard-sphere to Lennard-Jones-type clusters

A relation M_{SHS→LJ} between the set of nonisomorphic sticky-hard-sphere clusters M_{SHS} and the sets of local energy minima M_{LJ} of the (m,n)-Lennard-Jones potential V_{mn}^{LJ}(r)=ɛ/n-m[mr^{-n}-nr^{-m}] is established. The number of nonisomorphic stable clusters depends strongly and nontrivially on both m and n and increases exponentially with increasing cluster size N for N≳10. While the map from M_{SHS}→M_{SHS→LJ} is noninjective and nonsurjective, the number of Lennard-Jones structures missing from the map is relatively small for cluster sizes up to N=13, and most of the missing structures correspond to energetically unfavorable minima even for fairly low (m,n). Furthermore, even the softest Lennard-Jones potential predicts that the coordination of 13 spheres around a central sphere is problematic (the Gregory-Newton problem). A more realistic extended Lennard-Jones potential chosen from coupled-cluster calculations for a rare gas dimer leads to a substantial increase in the number of nonisomorphic clusters, even though the potential curve is very similar to a (6,12)-Lennard-Jones potential.