Atomistic Model of Uranium

The electronic state and potential data of U₂ molecules are performed by first principle calculations with B3LYP hybrid exchange-correlation functional, the valence electrons of U atom are treated with the (5s4p3d4f)/[3s3p2d2f] contraction basis sets, and the cores are approximated with the relativistic effective core potential. The results show that the ground electronic state is X⁹∑⁺_g . The pair potential data are fitted with a Murrell-Sorbie analytical potential function. The U-U embedded atom method (EAM) interatomic potential is deter-mined based on the generalized gradient approximation calculation within the framework of the density functional theory using Perdew-Burke-Ernzerhof exchange-correlation functional at the spin-polarized level. The physical properties, such as the cohesive energy, the lattice constant, the bulk modulus, the shear modulus, the sc/fcc relative energy, the hcp/fcc rela-tive energy, the shear modulus and the monovacancy formation energy are used to evaluate the EAM potential parameters. The U-U pair potential determined by the first principle calculations is in agreement with that defined by the EAM potential parameters. The EAM calculated formation energy of the monovacancy in the fcc structure is also found to be in close agreement with DFT calculation.     

Dendritic polyamine architectures with lipophilic shells as nanocompartments for polar guest molecules: A comparative study of their transport behavior

Dendritic core-shell architectures were synthesized by simple melt reactions of polyethylenimine (PEI) with different fatty acids. These systems were investigated towards their ability to encapsulate various guest molecules. Parameters, such as the length of the attached alkyl chain, size of the polymer core, concentration of the core-shell architecture in solution, pH, and nature of the guest molecule were investigated and compared. Guest molecules that bear anionic groups, such as carboxylate, phosphate, sulfonate, or acidic OH groups, as present in phenol units, are readily encapsulated and transferred from the aqueous phase to the organic phase because of multiple anionic–cationic interactions. Hyperbranched polymer architectures exhibit enhanced encapsulation properties when compared with their linear counterparts. In case of the hyperbranched system PEI₂₅C16 amide higher transport capacities were observed at lower concentrations of the polymer, for example, 26 guest molecules at 10⁻⁵ mol L⁻¹ versus 143 at 10⁻⁶ mol L⁻¹, suggesting formation of larger aggregates. The aggregation behavior of these polar nanocompartments were investigated at different concentrations by AFM showing particle aggregates of typically 250 nm at a concentration of 10⁻⁵ M. The individual particle sizes in these aggregates are similar to the particle size at 10⁻⁶ M concentration, typically 4.0–5.5 nm (AFM height). This indicates that aggregate formation takes place at concentrations higher than 10⁻⁸ M and transport might be mediated by small aggregates rather than unimolecular particles. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2287–2303, 2007     

Self-assembling of the porphyrin-linked acyclic penta- and heptapeptides in aqueous trifluoroethanol

The conjugates of porphyrin with links to the acyclic penta- and heptapeptides were synthesized to mimic natural multiple porphyrin systems. The linear penta- and heptapeptide with hydrophilic/hydrophobic alternative sequences took a random structure in aqueous trifluoroethanol (TFE). However, these polypeptides took a beta-sheet structure in the same solvent when the N-terminal Cys linked to the porphyrin, suggesting that the conjugates self-assembled via the intermolecular hydrophobic interaction between the porphyrins. The circular dichroism (CD) spectra, UV/vis spectra, size exclusion chromatography (SEC), and (1)H NMR spectroscopy supported the self-assembling. In the self-assembled structure of the pentapeptide linking porphyrin at the p-phenyl position (9), the porphyrins were involved in two porphyrin-porphyrin interactions, i.e., the side-by-side interaction between the neighboring polypeptide chains and the face-to-face interaction between the first and the third peptide chains. The CD spectra of 9 showed two sets of Cotton effects probably arising from these two interactions. The UV/vis spectra also supported the above interpretation, showing multiple absorptions in the longwave and shortwave shifted regions. The SEC analyses showed the assembled structure of the conjugates. The (1)H NMR signals of the porphyrin rings of 9 were hardly observed in D(2)O-CD(3)OD because of the shortened spin-spin relaxation time T(2)().     

Science-Driven Atomistic Machine Learning

Machine learning (ML) algorithms are currently emerging as powerful tools in all areas of science. Conventionally, ML is understood as a fundamentally data-driven endeavour. Unfortunately, large well-curated databases are sparse in chemistry. In this contribution, I therefore review science-driven ML approaches which do not rely on “big data”, focusing on the atomistic modelling of materials and molecules. In this context, the term science-driven refers to approaches that begin with a scientific question and then ask what training data and model design choices are appropriate. As key features of science-driven ML, the automated and purpose-driven collection of data and the use of chemical and physical priors to achieve high data-efficiency are discussed. Furthermore, the importance of appropriate model evaluation and error estimation is emphasized.     

Atomistic analysis of pseudoknotted RNA unfolding

As important functional structures, RNA pseudoknots provide excellent models for studying the interplay between secondary and tertiary structures and the roles of triplexes, noncanonical interactions, and coaxial stacking in the folding/unfolding process. Here we report a first atomistic and statistical analysis of the unfolding of the pseudoknot within gene 32 mRNA of bacteriophage T2. Multiple unfolding pathways, diverse transition states, and various intermediate structures were observed. Water molecules were found to be coupled with the unfolding process via the expulsion or concurrent mechanism.     

Atomistic theory of amyloid fibril nucleation

We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution. Our analysis illustrates the unique feature of ANT that the size of the fibril nucleus is a constant integer in a given supersaturation range. We obtain the ANT nucleation rate and compare it with the rates determined previously in the scope of the classical nucleation theory (CNT) and the corrected classical nucleation theory (CCNT). We find that while the CNT nucleation rate is orders of magnitude greater than the ANT one, the CCNT and ANT nucleation rates are in very good quantitative agreement. The results obtained are applicable to homogeneous nucleation, which occurs when the protein solution is sufficiently pure and/or strongly supersaturated.     

Atomistic modeling of enantioselection in chromatography

A review of atomistic molecular modeling studies related to chromatographic separations of enantiomers is presented. Only those types of calculations where direct interactions between a selector and a selectand are involved are described in this review; omitted are regression models. An emphasis is placed on comparing methods used for sampling potential energy surfaces implementing different methodologies like quantum and molecular mechanics for energy calculations, and molecular dynamics and Monte Carlo sampling strategies for simulations. Type I-V chiral stationary phases and additives for capillary electrophoresis and ion-pair chromatography are covered in this review.     

Synthesis of heptapeptides and analysis of sequence by tandem ion trap mass spectrometry

Two heptapeptides have been prepared by Fmoc methodology using Wang resin as solid support. For attachment of the first amino acid, several coupling systems were evaluated, and DIC/DMAP system could give yields of >99% and low levels of racemization. The selection of scavenger combination to deprotect side chains revealed that H₂O/p-cresol was good at scavenging trityl and 1,2-ethanedithiol was highly efficient for scavenging t-butyl. Through shortening the preactivation time to 5 min, the racemization which occurred during formation of amide bonds coupled by HBTU was minimized. The crude peptides were characterized by RP-HPLC and MS, and sequenced by MS/MS to acquire reliable amino acid sequence information.     

Atomistic calculations of crystal structures of polyisobutylene

Semiempirical atomistic calculations are performed to investigate the crystalline structure of stretched poly(1,1-dimethylethylene), or polyisobutylene. The packing analysis was done without any lattice symmetry assumptions. The results are in good agreement with the x-ray analysis and favor Tanaka's model II. The calculations show several other crystalline structures with the chains in an all-gauche conformation. They have a somewhat higher density and may play a role in a hypothetical high-pressure phase of polyisobutylene.Dedicated to Prof. Dr. W. Pechhold on the occasion of his 60th birthday     

Novel architectures of boron

Structural Chemistry - The review presents results of the recent studies of non-typical forms of boron derivatives, including flat hexagonal boron, boron fullerenes, supertetrahedral boron, and...     

Atomistic mechanism of protein denaturation by urea

Effects of urea on protein stability have been studied from all-atom molecular dynamics simulations of ubiquitin, G311 protein, and immunoglobulin binding domain (B1) of streptococcal protein G (GB1) in water and 8 M aqueous urea solution. The mechanism of the change in the solvent environment and the early events in protein unfolding by urea have been identified with emphasis on the change in the interactions of hydrophilic and hydrophobic parts of the protein by calculating the potential of mean force (PMF). Urea replaces the protein-protein and protein-water contacts by forming stronger contacts with the protein, which is indicated by the longer survival times of the protein-urea hydrogen bonds.     

Atomistic insights into aqueous corrosion of copper

Corrosion is a fundamental problem in electrochemistry and represents a mode of failure of technologically important materials. Understanding the basic mechanism of aqueous corrosion of metals such as Cu in presence of halide ions is hence essential. Using molecular dynamics simulations incorporating reactive force-field (ReaxFF), the interaction of copper substrates and chlorine under aqueous conditions has been investigated. These simulations incorporate effects of proton transfer in the aqueous media and are suitable for modeling the bond formation and bond breakage phenomenon that is associated with complex aqueous corrosion phenomena. Systematic investigation of the corrosion process has been carried out by simulating different chlorine concentration and solution states. The structural and morphological differences associated with metal dissolution in the presence of chloride ions are evaluated using dynamical correlation functions. The simulated atomic trajectories are used to analyze the charged states, molecular structure and ion density distribution which are utilized to understand the atomic scale mechanism of corrosion of copper substrates under aqueous conditions. Increased concentration of chlorine and higher ambient temperature were found to expedite the corrosion of copper. In order to study the effect of solution states on the corrosion resistance of Cu, partial fractions of proton or hydroxide in water were configured, and higher corrosion rate at partial fraction hydroxide environment was observed. When the Cl(-) concentration is low, oxygen or hydroxide ion adsorption onto Cu surface has been confirmed in partial fraction hydroxide environment. Our study provides new atomic scale insights into the early stages of aqueous corrosion of metals such as copper.     

Chloride complexation by heptapeptides: influence of C- and N-terminal sidechains and counterion

The channel-forming diglycolylated heptapeptides containing the amino acid sequence Gly-Gly-Gly-Pro-Gly-Gly-Gly have been found to complex chloride in CDCl(3). The strength of the interaction depends on the terminal alkyl groups and on chloride's countercation.