Peculiarities of interactions between the DNA molecule and different isomers and modifications of binuclear coordination compounds of platinum(II)

A comparison has been made of conformational changes in the DNA molecule during its interaction in solution with different binuclear coordination compounds of platinum [Pt(NH₃)₂Cl-R-Pt(NH₃)₂Cl]Cl₂ in cis and trans conformations, which contain cytosine, pyrazine, and carboxypyrazine as the common ligand (R). The influence of concentration of the components, and in particular, of ionic strength of the solution on the complexation process was studied. The influence of the nature of the common ligand, and of cis and trans conformations of coordination compounds on the character of their interaction with DNA was considered. A comparison was made between the structures of DNA complexes with mono-and binuclear compounds with the same set of ligands in the platinum coordination sphere.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Ab initio and DFT calculations on the initial step in thiamin catalysis

The diphosphate ester (ThDP) of thiamin (vitamin B₁) is an important cofactor of enzymes within the carbohydrate metabolism. The initial reaction step shared by all ThDP-dependent enzymes is the deprotonation of the C2–H of the thiazolium ring. The replacement of the 4′-amino group by a hydroxyl one in the pyrimidine ring leads to the oxy-ThDP analogue which is known as an antagonist in thiamin catalysis.

Ab initio and DFT calculations on the MP2/6-31G* and B3LYP/6-31G* level were performed to study the proton relay function in thiamin and oxythiamin systems. Both MP2 and B3LYP calculations show significant differences of the reaction coordinate of the ylide formation in the systems. Tautomers, protonated and deprotonated species of both systems show different trends regarding their stability. The influence of correlation effects on the results is discussed by comparison with the HF-SCF/6-31G* data. Frequency calculations on the B3LYP/6-31G* level were performed to characterize the minima and transition state structures, respectively.     

H2 + CN(n=0,1)→H + HCN振动选态反应

用从头算方法获得了Ｈ２＋ＣＮ反应的内禀反应坐标（ＩＲＣ），沿着ＩＲＣ，计算了各垂直于ＩＲＣ的简正模所对应的频率（Ｗ）以及沿ＩＲＣ运动与垂直ＩＲＣ运动的简正模之间的耦合常数（ＢＫＦ），根据传统过渡态，变分过渡态理论和选态公式，计算了ｎＣＮ＝０及ｎＣＮ＝１时反应的速率常数，并得到了实验相一致的结果，还计算了ｎＣＨ＝１及ｎＣＮ＝１的Ｈ＋ＨＣＮ→Ｈ２＋ＣＮ反应速率常数，可供实验工作者参考。     

Synthesis and Crystal Structure of a 1D Chained Coordination Polymer Containing One-dimensional Egg-like Channels： {[Cu2（C2O4）2（inta）4]（inta）}n （inta = Isonicotinamide）

A new one-dimensional copper coordination polymer chain has been prepared and fully characterized by single-crystal X-ray diffraction,elemental analyses and IR spectroscopy. The compound {[Cu2(C2O4)2(inta)4](inta)}n1 crystallizes in the triclinic system,space group P1,with a=8.4722(5),b=10.9825(6),c=11.6128(6),α=104.8050(10),β=102.5740(10),γ= 109.6890(10)o,V=927.18(9)3,Mr=929.79,Z=1,Dc=1.665 g/cm3,F(000)=475,μ=1.231 mm-1,R=0.0453 and wR=0.1185 for 3290 observed reflections (I > 2σ(I)). Of the compound,the Cu center is octahedrally coordinated with oxalate acting as a tetra-dentate ligand coordinated to the copper atom and each inta serving as a terminal ligand by employing only one N-donor to coordinate with the Cu center. An infinite {Cu2(C2O4)2}∞ chain is formed along the c axis. Furthermore,the 1D chains are held together via extensive hydrogen-bonding interactions to generate a three-dimensional network with 1D channels (ca. 5.491×11.507) where inta molecules are filled.     

Coordinate Structures of PrIII, GdIII, TmIII, and YbIII Complexes with Nitrilotriacetic Acids

The crystal and molecular structures of the [Pr^III(nta)(H₂O)₂]·H₂O (nta = nitrilotriacetic acids), K₃[Gd^III(nta)₂(H₂O)]·6H₂O, and K₃[Yb^III(nta)₂]·5H₂O complexes have been determined by single-crystal X-ray structure analyses. In [Pr^III(nta)(H₂O)₂]·H₂O, the Pr^IIINO₈ part forms a nine-coordinate pseudo-monocapped square antiprismatic structure in which one N and three O atoms are from one nta ligand in the same molecule, three O atoms from another nta ligand in the neighboring molecule and two O atoms from two coordinate water molecules. In K₃[Gd^III(nta)₂(H₂O)]·6H₂O, the [Gd^III(nta)₂(H₂O)^3- complex anion has a nine-coordinate pseudo-monocapped square antiprismatic structure in which each nta acts as a tetradentate ligand with one N atom of the amino group and three O atoms of the carboxylic groups. In K₃[Yb^III(nta)₂]·5H₂O, each nta also acts as a tetradentate ligand with one N atom of amino group and three O atoms of the carboxylic groups, but the [Yb^III(nta)₂ ^3- complex anion has an eight-coordinate structure with a distorted square antiprismatic prism. All the results including those for [Tm^III(nta)(H₂O)₂]·2H₂O confirm the inferences on the coordinate structures and coordination numbers of rare earth metal complexes with the nta ligand.     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

Active transient elasto-acoustic response damping of a thick-walled liquid-coupled piezolaminated cylindrical vessel

The linear 3D piezoelasticity theory in conjunction with the versatile transfer matrix approach and the wave equation for the internal acoustic domain are employed for active non-stationary vibroacoustic response control of an arbitrarily thick, tri-laminate, fluid-filled, simply supported, piezocomposite cylindrical tank, excited by arbitrary (non-axisymmetric) time-dependent on-surface mechanical loads. The smart structure is composed of a supporting core layer of functionally graded orthotropic material perfectly bonded to inner and outer spatially distributed radially polarized functionally graded piezoceramic sensor and uniform force actuator (FGPM) layers. Active vibration damping is implemented by transferring the accumulated voltage on the sensor layer to the piezoelectric actuator layer in context of proportional and derivative control laws. Durbin's numerical inverse Laplace transform scheme is utilized to calculate the time response histories of the relevant interface displacement/stress components, center-point acoustic pressure, and actuator voltage, for selected loading configurations (i.e., concentrated step, impulse, and moving external loads). Numerical simulations demonstrate the effectiveness of the adopted distributed sensing/actuation configuration together with the active damping control strategy in suppressing the vibroacoustic response of a three-layered (Ba₂NaNb₅O₁₅/Al/PZT4) water-filled piezoelastic cylindrical tank. Limiting cases are considered and the validity of results is established by comparison with the available data as well as with the aid of a commercial finite element package.     

FOURIER-TRANSFORM RAMAN AND INFRARED SPECTRA AND VIBRATIONAL ASSIGNMENT FOR SOLID GLUTARIMIDE

Abstract

The FT-Raman and FT-IR spectra of crystalline glutarimide and its N-deuterated derivative have been recorded in the range 4000-100 cm^?1. A complete vibrational assignment is given for all internal modes and is supported by normal coordinate analysis based on a general valence force field. The calculated frequencies are in very good agreement with experiment. A close similarity is found for frequencies of the corresponding vibrations of glutarimide and uracils in the solid state. It is concluded that the strength of hydrogen bonding in glutarimide is very similar to that in crystalline pyrimidine nucleic bases.     

Global attractor for the Navier–Stokes equations with the heat convection in a cylindrical pipe

Global existence of regular solutions to the Navier–Stokes equations coupled with the heat convection in a cylindrical pipe has already been shown. In this paper, we prove the existence of the global attractor to the equations and convergence of their solutions to a stationary one. Copyright © 2012 John Wiley & Sons, Ltd.