Data parallel large-scale molecular dynamics for liquids

An efficient data parallel computational scheme is presented for large-scale molecular dynamics (MD ) simulations of liquids with short-range interactions. The method is based on decomposition of the simulation cell into equally sized subcells, with the shortest side length equal to the cutoff radius. Inter- and intracell interactions are calculated in a coarse-grained manner. A geometric sorting procedure, based on particle distances to subcell boundaries, is used to minimize the overall computations and the nonproductive communications. Using only nearest-neighbor communications, an efficient scheme is developed for periodic updates of the contents of subcells due to the migration of particles. Special “null-particles” are introduced, which act as buffers during the periodic updates and allow for a globally uniform algorithm during the calculations. Communication cost is about 7% of the total CPU time. The method is found to be linearly scalable with the number of particles, performing better as the ratio of virtual to physical processors increases. The MD code is written in Fortran 90 and implemented on a CM-200. The overall speed is approximately 5.9 μs. per MD step and per particle for 1 million particles and 5.5 μs for 5 million particles. The method should be easily transferred to other massively parallel computers of SIMD and MIMD type. © 1993 John Wiley & Sons, Inc.     

Feature vector clustering molecular pairs in computer simulations

A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P_6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.     

GC–MS with photoionization of cold molecules in supersonic molecular beams—Approaching the softest ionization method

A new type of photoionization ion source was developed for the ionization of cold molecules in supersonic molecular beams (named Cold PI). The system was based on a GC–MS with supersonic molecular beams and its fly‐through EI of cold molecules ion source (Cold EI) plus quadrupole mass analyzer. A continuously operated deuterium VUV photoionization lamp was added and placed above and between the supersonic nozzle and skimmer whereas the Cold EI ion source served only as a portion of the ion transfer ion optics. The supersonic nozzle and skimmer were voltage biased and the VUV light crossed the supersonic expansion about 10 mm from the nozzle. We obtained over three orders of magnitude enhancement in the relative abundance of the molecular ion of squalane in Cold PI versus in photoionization of this compound as a thermal compound. Accordingly, we also proved that standard photoionization is not as soft ionization method as previously perceived for large compounds. We found that Cold PI is as soft as and possibly softer than field ionization; thus, it could be the softest known ionization method. The ionization yield was about 200–300 times weaker than with Cold EI yet our limit of detection was about 200 femtogram in SIM mode for cholesterol and pyrene which is reasonable. Practically, all hydrocarbons gave only molecular ions with rather uniform response whereas alcohols gave some molecular ions plus major fragment ions particularly with a loss of water (similarly to field ionization). We tested Cold PI in the GC–MS analysis of diesel fuels and analyzed the time averaged data for group type information. We also found that we can analyze the diesel fuels by fast under 20‐s flow injection analysis in which the generated averaged mass spectrum of molecular ions only could serve for the characterization of fuels.     

Gas phase photoisomerization of urocanic acid – a theoretical study

The photochemistry of urocanic acid is investigated theoretically by means of time-dependent density functional theory. The topology of the potential energy surface along the isomerization pathway and close to the Franck–Condon region is investigated and consequences for the photoisomerization reactions are outlined. A recently published supersonic jet spectroscopy study is reinterpreted in the light of these and earlier theoretical results to give a clear picture of the gas phase photochemistry. It is found that the photochemistry of the two isomers is fundamentally different, in contrast to the situation in solution.     

Ion permeability of SAMs on nanoparticle surfaces

This article reports on the ion permeability of self-assembled monolayers (SAMs) formed on the surface of charged alkanethiol-protected gold nanoparticles, so-called monolayer-protected clusters (MPCs). The capacitance and thus the charging energy required to add/remove an electron from the metal core are extremely sensitive to ions entering the monolayer, and the extent of ion penetration can be tuned by the charge and size of the ions and the permittivity of the solvent. Experimentally, this effect is comparable to ion association with conventional redox molecules, indicating that MPCs despite their large size and the fundamentally differing nature of the electron transfer process can be treated analogously to redox molecules.     

Carbohydrates Exhibit a Distinct Preferential Solvation Pattern in Binary Aqueous Solvent Mixtures

Molecular dynamics simulations reveal the entire solvation shell around a model disaccharide dissolved in the binary 1:3 molar mixture of dimethyl sulfoxide and water becomes distinctly structured (see drawing). Such preferential solvation is due to the large number of hydroxyl groups and the rich network of hydrogen bonds of a disaccharide formed with the solvent.     

Solvating,manipulating, damaging,and repairing DNA in a computer

This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution

Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.