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     

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.     

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.     

Complete-active-space self-consistent-field/Amber parameterization of the Lys296–retinal–Glu113 rhodopsin chromophore-counterion system

A special hybrid quantum mechanics/molecular mechanics forcefield is defined, parameterized and validated for studying the photoisomerization path of the retinal chromophore in the rhodopsin protein. It couples a multireference ab initio Hamiltonian (CASSCF and second-order multireference many-body perturbation theory using a CASSCF reference) to describe the chromophore while the rest of the protein is approximated with the Amber forcefield. The frontier has been carefully parameterized in order to reproduce full quantum mechanics torsional energy profiles, for both the ground state and the first excited state. It is also shown that replacing the chromophore counterion with point charges is a valid approximation. This result is interpreted in terms of a cancellation effect for which a possible explanation is given.     

铝酸钠溶液的紫外吸收峰

分别用量子化学MNDO和DV-X_α方法计算了二聚铝酸离子[Al_2O(OH)_6]~(2-)和Al(OH)_4~-。结果表明前者旋转势垒很低, 只有10.08 kJ·mol~(-1), 最稳定平衡构型为C_s。用X_α过渡态理论计算获得这两个离子紫外吸收峰的理论值分别为266.6 nm和234.4 nm, 与实验值270.0 nm和230.0 nm相当接近。因此可以认为, 紫外吸收峰270.0 nm和230.0 nm分别为[Al_2O(OH)_6]~(2-)和Al(OH)_4~-离子的最高占有轨道电子向最低空轨道跃迁时产生的吸收峰。计算结果支持铝酸钠溶液中存在二聚铝酸离子的观点。     

四甲基对联苯二胺光敏化聚苯乙烯砜及其模型化合物二苄基砜分解机理的研究

N、N、 N’、N’-四平基对联苯二胺(NTMB)和 3、3’、5、5’-四甲基对联苯二胺(TMB)可以有效地光敏化二苄基砜(DBS)分解和聚苯乙烯砜(PSS)降解。敏化作用是按电子转移机理进行的,电子转移过程可以由NTMB的单重激发态,也可以由三重激发态发生。由三重态电子转移产生的三重态离子自由基对进一步反应生成产物的效率比单重态离子自由基对的效率高10倍。     

Uniqueness and clustering properties of Gibbs states for classical and quantum unbounded spin systems

We consider quantum unbounded spin systems (lattice boson systems) in -dimensional lattice space Z. Under appropriate conditions on the interactions we prove that in a region of high temperatures the Gibbs state is unique, is translationally invariant, and has clustering properties. The main methods we use are the Wiener integral representation, the cluster expansions for zero boundary conditions and for general Gibbs state, and explicitly -dependent probability estimates. For one-dimensional systems we show the uniqueness of Gibbs states for any value of temperature by using the method of perturbed states. We also consider classical unbounded spin systems. We derive necessary estimates so that all of the results for the quantum systems hold for the classical systems by straightforward applications of the methods used in the quantum case.