Modeling of serine protease prototype reactions with the flexible effective fragment potential quantum mechanical/molecular mechanical method

A complete cycle of chemical transformations for the serine protease prototype reaction is modeled following calculations with the flexible effective fragment quantum mechanical/molecular mechanical (QM/MM) method. The initial molecular model is based on the crystal structure of the trypsin–bovine pancreatic trypsin inhibitor complex including all atoms of the enzyme within approximately 15–18 Å of the oxygen center O of the catalytic serine residue. Several selections of the QM/MM partitioning are considered. Fractions of the side chains of the residues from the catalytic triad (serine, histidine and aspartic acid) and a central part of a model substrate around the C–N bond to be cleaved are included into the QM subsystem. The remaining part, or the MM subsystem, is represented by flexible chains of small effective fragments, whose potentials explicitly contribute to the Hamiltonian of the QM part, but the corresponding fragment–fragment interactions are described by the MM force fields. The QM/MM boundaries are extended over the C–C bonds of the peptides assigned to the QM subsystem in the enzyme, C–C and C–N bonds in model substrates. Multiple geometry optimizations have been performed by using the RHF/6-31G method in the QM part and OPLSAA or AMBER sets of MM parameters, resulting in a series of stationary points on the complex potential-energy surfaces. All structures generally accepted for the serine protease catalytic cycle have been located. Energies at the stationary points found have been recomputed at the MP2/6-31+G^* level for the QM part in the protein environment. Structural changes along the reaction path are analyzed with special attention to hydrogen-bonding networks. In the case of a model substrate selected as a short peptide CH₃(NHCO-CH₂)₂ – HN–CO–(CH₂–NHCO)CH₃ the computed energy profile for the acylation step shows too high activation energy barriers. The energetics of this rate-limiting step is considerably improved, if more realistic model for the substrate is considered, following the motifs of the ThrI11–GlyI12–ProI13-–CysI14–LysI15–AlaI16–ArgI17–IleI18–IleI19 sequence of the bovine pancreatic trypsin inhibitor.     

DNA-mediated coordinative assembly of upconversion hetero-nanostructures for targeted dual-modality imaging of cancer cells

We reported a simple and universal strategy for DNA-mediated assembly of CdTe quantum dots (QDs) and lanthanide-doped upconversion nanoparticles (UCNPs). Such DNA-QD/UCNPs heterostructures not only maintains both fluorescent properties of QDs and upconversion luminescence behaviors of UCNPs, but also offers a polyvalent DNA surface, allowing for targeted dual-modality imaging of cancer cells using an aptamer     

Electronic spectral and photophysical properties of some p-phenylenevinylene oligomers in solution and thin films

A comprehensive photophysical and spectroscopic study of a new class of p-phenylenevinylene oligomers (PPV-trimers) possessing different alkyl and alkyloxy sidechain substituents and different end groups (aldehyde, CC, phenylene and anthracene units) was undertaken in solution at room temperature (293 K), low temperature (77 K) and in thin films. The study comprises absorption, emission and triplet–triplet absorption spectra, together with quantitative measurements of quantum yields (fluorescence, intersystem crossing, internal conversion and singlet oxygen formation) and lifetimes. The data allow the determination of rate constants for all decay processes. From these, several conclusions could be drawn. Changing from alkyl to alkyloxy substituents does not change fluorescence and internal conversion yields but decreases the (already small) intersystem crossing yield. The introduction of anthracene at the terminal ends of the PPV-trimers leads to the lowest fluorescence yield reported in this study. Of particular importance is the fact that the fluorescence quantum yields in films are of the same order of magnitude as those in solution, which suggests the potential for use of these oligomers for light-emitting device applications. With one of the alkyloxy derivatives, a more detailed study of the early part of the fluorescence decay was made, and it was found that upon excitation a fast conformational relaxation process of the initially excited oligomer occurs, leading to a more planar conjugation segment.     

Structural Analysis of Ti And Pb Citrate Using NMR and FT-Raman Signals and Quantum Mechanics Simulations

Titanium citrate and lead and titanium citrate were prepared by polymeric precursor method in aqueous solution. This citrate was analyzed by ¹H, ¹³C NMR and gHMBC–NMR (Hetero-nuclear multiple-bond correlation) to investigate the formation of the citrate complexs and influence of the Pb²⁺ ion in this complex. These complexs were characterized by interaction between Ti⁴⁺ ion and citric acid carboxyls. Quantum mechanic simulations in level ab initio were used to study the electronic structure and natural charges (NBO) to both the complexs. Such techniques indicated the formation of an octahedral complex with an arrangement similar to Ti atom in the crystalline structure of the PbTiO₃. A study using the technique FT-Raman made possible the confirmation of the interaction among the Ti⁴⁺ and Pb²⁺ ions with the citric acid carboxyls.     

Atomic structure of InAs quantum dots on GaAs

In recent years, the self-assembled growth of semiconductor nanostructures, that show quantum size effects, has been of considerable interest. Laser devices operating with self-assembled InAs quantum dots (QDs) embedded in GaAs have been demonstrated. Here, we report on the InAs/GaAs system and raise the question of how the shape of the QDs changes with the orientation of the GaAs substrate. The growth of the InAs QDs is understood in terms of the Stranski–Krastanow growth mode. For modeling the growth process, the shape and atomic structure of the QDs have to be known. This is a difficult task for such embedded entities.

In our approach, InAs is grown by molecular beam epitaxy on GaAs until self-assembled QDs are formed. At this point the growth is interrupted and atomically resolved scanning tunneling microscopy (STM) images are acquired. We used preparation parameters known from the numerous publications on InAs/GaAs. In order to learn more about the self-assemblage process we studied QD formation on different GaAs(0 0 1), (1 1 3)A, and ( )B substrates. From the atomically resolved STM images we could determine the shape of the QDs. The quantum “dots” are generally rather flat entities better characterized as “lenses”. In order to achieve this flatness, the QDs are terminated by high-index bounding facets on low-index substrates and vice versa. Our results will be summarized in comparison with the existing literature.     

Self-assembled luminescent CdSe-ZnS quantum dot bioconjugates prepared using engineered poly-histidine terminated proteins

We report a simple and versatile approach for the conjugation of luminescent CdSe-ZnS core-shell quantum dots (QDs) to proteins through coordination of engineered C-terminal oligohistidine sequences. Several histidine tail containing proteins were self-assembled onto the QD surface using this method. A recombinant antibody specific for the high explosive 2,4,6-trinitrotoluene (TNT) was conjugated to QDs through a carboxy terminal histidine tail and the bioconjugate used to detect TNT by competitive immunoassay. TNT was detected over the range of 10 μg/ml down to 41 ng/ml using the scFv conjugated to QDs. These results open up the possibility to conjugate luminescent QDs to a whole range of proteins to form QD bioconjugates that can be effectively used in bio-oriented applications, such as sensing, imaging, immunoassay and other diagnostics.     

Laser field induced charge transfer: Para-nitroaniline coupled to a quantum mechanical radiation field

Summary We present a preliminary model for describing a solvated intramolecular charge transfer reaction coupled to a quantum mechanical radiation field. Actual calculations of energies and couplings were performed with a recently developed self-consistent reaction field response method. The representation of dressed molecular states is used for calculating state populations for various laser fields. The state populations are sensitive to the properties of the laser field.     

Quantum chemical modeling for 157 nm photolithography

In its continuing quest for smaller length scales, the electronics industry plans to introduce 157 nm as the next lithographic wavelength. Accordingly, there is a pressing need to develop photoresists that are more transparent, and pellicles that are both more transparent and more durable. With the advent and popularization of time-dependent density functional theory (TD-DFT), we now have a practical quantum chemical method for calculating excitation energies and transition moments in the vacuum ultraviolet (VUV) which can greatly assist in the scouting of highly transparent materials. We have performed TD-DFT calculations for a broad variety of fluorinated molecules and we will report calculated VUV photoabsorption spectra for a large family of model fluorohexanes. These calculations, which span a range from 1-fluorohexane to CH₃CF₂CF₂CF₂CF₂CH₃, illustrate some of the principles one may use to design low absorption polymeric materials.     

Computation of cross sections for the F+H2(v=0,j=0) → FH(v′j)+H reaction by the hyperspherical method

Summary A quantum mechanical calculation of cross sections for the reaction F+H₂(v=0,j=0) FH(vj)+H has been performed on the T5A semiempirical potential surface using hyperspherical coordinates. State-to-state integral and differential cross sections converge rapidly with the number of components of the total angular momentum projection onto the axis of least inertia. Thev=3 differential cross section has a forward peak whose magnitude increases with energy whereas thev=2 differential cross section has a backward maximum, in qualitative agreement with cross-beam experiments. Thev=2 andv=3 rotational distributions are in rather good agreement with experiment, but not the vibrational branching ratios.