Structure of cis-[Pt(NH_3)(2-picoline)]~(2+) and DNA adduct and its bonding characteristics

Several methods including molecular mechanics, molecular dynamics, ONIOM that combines quantum chemistry with molecular mechanics and standard quantum chemistry are used to study the configuration and electron structures of an adduct of the DMA segment d(ATACATG*G*TACATA)-d(TATGTACCATGTAT) with cis-[Pt(NH3)(2-Picoline)]2+. The investigation shows that the configuration optimized by ONIOM is similar to that determined by NMR. Strong chemical bonds between Pt of the complex and two N7s of neighboring guanines in the DNA duplex and hydrogen bond between the NH3of the complex and O6 of a nearby guanine have a large impact on the configuration of the adduct. Chemical bonds, the aforementioned hydrogen bond, and the interaction between a methyl of the complex and a methyl of the base in close proximity are critical for the complex to specifically recognize DNA.     

Proteomics and Its Application in Biomarker Discovery and Drug Development

Proteomics is a research field aiming to characterize molecular and cellular dynamics in protein expression and function on a global level. The introduction of proteomics has been greatly broadening our view and accelerating our path in various medical researches. The most significant advantage of proteomics is its ability to examine a whole proteome or sub-proteome in a single experiment so that the protein alterations corresponding to a pathological or biochemical condition at a given time c…     

Influence of temperature on the structure of liquid water

Molecular dynamics simulations have been carried out for liquid water at 7 different temperatures to understand the nature of hydrogen bonding at molecular level through the investigation of the effects of temperature on the geometry of water molecules. The changes in bond length and bond angle of water molecules from gaseous state to liquid state have been observed, and the change in the bond angle of water molecules in liquid against temperature has been revealed, which has not been seen in literature so far. The analysis of the radial distribution functions and the coordinate numbers shows that, on an average, each water molecule in liquid acts as both receptor and donor, and forms at least two hydrogen bonds with its neigbors. The analysis of the results also indicates that the water molecules form clusters in liquid.     

Infrared Spectra and Pyrolysis of Selected Molecular Models of Coal: Insight from Density Functional Calculations

Equilibrium structures and infrared spectra of four typical molecular models of coal have been studied by density functional calculations. Combining theoretical calculations on the coal models with experimental FT-IR spectra of selected low rank perhydrous coals, a plausible molecular representation for this kind of coals was proposed, and its predicted IR spectra reasonably match the experimental observation. Calculations indicate that the cleavage of the C-C bridge bond for the coal structures considered here occurs at about 540 ℃ and the C-O ether bridge bond may break under temperature ranging from 500 to 600 ℃ for the aryl-CH2-O-CH2-aryl ether bond or from 200 to 300 ℃ for the aryl-CH2-O-aryl ether bond, showing remarkable effect of the local structural environment. The coal model containing the carboxyl group may release CO2 at about 300 ℃ through the decarboxylation with a barrier of 69 kcal/mol.     

Theoretical Investigations on the Structure,Density, Thermodynamic and Performance Properties of Bis（2,2-dinitropropyl） formal

Density functional method was used to investigate the IR spectrum,heat of formation and thermal stability of a new energetic material bis(2,2-dinitropropyl) formal(BDNPF).The detonation velocity and pressure were evaluated by using the Kamlet-Jacobs equations based on the theoretical density and heat of formation.The bond dissociation energies for the weakest bonds were analyzed to investigate the thermal stability of the title compound.The results show that the C(1)-N(1) bond is predicted to be the trigger bond during pyrolysis.The crystal structure obtained by molecular mechanics belongs to the P21 space group,with the lattice parameters to be Z = 2,a = 11.5254,b = 6.2168,c = 9.5000  and ρ= 1.66 g/cm3.     

Dynamical and allosteric regulation of photoprotection in light harvesting complex Ⅱ

Major light-harvesting complex of photosystem Ⅱ(LHCⅡ) plays a dual role in light-harvesting and excited energy dissipation to protect photodamage from excess energy. The regulatory switch is induced by increased acidity, temperature or both. However,the molecular origin of the protein dynamics at the atomic level is still unknown. We carried out temperature-jump time-resolved infrared spectroscopy and molecular dynamics simulations to determine the energy quenching dynamics and conformational changes of LHCⅡ trimers. We found that the spontaneous formation of a pair of local α-helices from the 310-helix E/loop and the C-terminal coil of the neighboring monomer, in response to the increased environmental temperature and/or acidity, induces a scissoring motion of transmembrane helices A and B, shifting the conformational equilibrium to a more open state, with an increased angle between the associated carotenoids. The dynamical and allosteric conformation change leads to close contacts between carotenoid lutein 1 and chlorophyll pigment 612, facilitating the fluorescence quenching. Based on these results, we suggest a unified mechanism by which the LHCⅡ trimer controls the dissipation of excess excited energy in response to increased temperature and acidity, as an intrinsic result of intense sun light in plant photosynthesis.     

Structural Properties of Nitromethane Molecular Crystal under High Pressure： An ab initio Investigation

The pressure-dependent structural properties under hydrostatic pressure up to 120 GPa and the decomposition under uniaxial compression along the b lattice vector up to 40 GPa of nitromethane molecular crystal using ab initio method are presented. The internal molecular bond lengths and bond angles were calculated for different pressures. All bond lengths decrease as the pressures are increased under hydrostatic compression. The obvious rotation of methyl group is 33.89° under hydrostatic pressure at 120 GPa. In addition, we observe the change of C-H bonds, which have been stretched under uniaxial compression along b lattice vector in the range of 0-40 GPa of nitromethane.     

The role of 3d orbitals in the bonding of phosphorus compounds

Ab initio LCAO-MO-SCF calculations for several typical molecules containing phosphorushave been undertaken to study the role of phosphorus 3d orbitals in the bonding.It is emphasizedthat the discussion about the 3d orbital participation in bonding should be based on a reasonable choiceof basis sets and it seems suitable to choose the atomic orbitals in proper molecular environment asthe basis set.As an approximation,the optimized minimal STO-NG basis sets have been adoptedin the present paper.The results obtained well exhibit the model of 3d orbital participation in bonding.It is shown that under the influence of highly electronegative ligands the phosphorus 3d orbitals con-tract greatly,their energy levels drop considerably,and thus they can effectively participate in bond-ing.The presence of highly electronegative ligands seems necessary.The contribution of 3d orbitalsto bonding is achieved mainly through the concertedformation of σ bonds and p-d backbonds,thoughthe contribution to σ bonding is minor.The three-center,four-electron bond modelis only approxi-mately correct.The results of the present paper demonstrate that the model of 3d orbital participationin bonding favoured by experimental chemists is reasonable and possesses sound ground.     

An MP2 study on pre-reactive complexes (CH_2)_2O … XY (X,Y = H,F,Cl,Br,I)

The structures, energies, atomic chaiges and IR spectra of complexes (CH2)2O…XY (X, Y = H, F, Cl, Br, and I) have been examined by means of ab initio molecular orbital theory at the second-order level of Moller-Plesset perturbation correction. It is found that the hydrogen bond O…H-X is non-linear. The attraction between X and the H atoms in oxirane ring causes O…H-X bond bending. The hydrogen bond slighdy weakens the bond strength of C-O, and leads the bending and stretching mode of IR to shift to the red. The calculation results show that there is no evidence of a significant extent of proton transfer to give (CH2)2OH …X- in the isolated complexes.     

Distribution and forms of phosphorus in tidal flat sediments of the Yangtze Estuary and coast

The distribution and forms of phosphorus (P) were investigated in the tidal flat sediments of the Yangtze Estuary and coast. The total P contents in surface sediments range from 18.0 to 31.4 μmol · g-1 along the southern coast. The spatial and temporal distribution of P in tidal flats is closely related to the location and pollution resources, especially in association with the variation of hydrodynamic conditions. Significant variations in the forms of P in different sites were observed. P bonded with Ca(Ca-P) is the dominant mineral form in all surface sediments, organic P(Org-P) is lower. Most P is of unstable form, suggesting that P has larger potential activity. P accumulation is the main behavior process between water and sediment in the coastal environment of the Yangtze Estuary.     

Valence bond description for structures of O_3, SO2 and NO_2~-

A modern valence bond approach, namely bonded tableau unitary group approach, isapplied to ozone, sulphur dioxide and nitrite systems, respectively. It is shown that the biradicalstructure is in the primary position in descrbing the molecular structure of ozone. Thus threeinstead of two resonance structures are needed to describe the ground state of ozone. The caseof sulphur dioxide is similar to that of ozone. It is found that, however, for the nitrite anion fourresonance structures are needed.     

Theoretical Investigation on the Geometries and Properties of Guanine-BX3 （X = F, Cl） Complex

Geometries and binding energies were predicted at the B3LYP/6-311+G* level for the guanine-BX3 (X = F, Cl) systems and four isomers with no imaginary frequencies have been obtained for both guanine-BF3 and guanine-BCl3, respectively. Single energy calculations using much larger basis sets (6-311+G(2df,p) and aug-cc-pVDZ were carried out as well. It was found that the most stable isomer of guanine-BF3 is BF3 connected to N3 of guanine with the stabilization energy of –19.93 kcal/mol (BSSE corrected), while that of guanine-BCl3 is BCl3 connected to O10 of guanine having stabilization energy of –15.02 kcal/mol at the same level. The analyses for the combining interaction between BX3 and guanine with the atom-in-molecules theory (AIM) and natural bond orbital (NBO) methods have been performed. The results indicated that all the isomers are formed with σ-p type interactions between guanine and BX3, in which pyridine-type nitrogen or carbonyl oxygen or nitrogen atom of amino group offers its lone pair electrons to the empty p orbital of boron atom and the concomitance of charge transfer from guanine to BX3 has occurred. Still, one or two hydrogen bonds exist in some isomers of guanine-BX3 system and contribute to the stability of complex systems. Frequency analysis suggested that the stretching vibration of BX3 undergoes a red shift in complexes. Guanine-BF3 complex is more stable than guanine-BCl3 although the B–Y (Y=N, O) bond distance in the latter is shorter.     

Molecular and quantum mechanical studies on the monomer recognition of a highly-regular β-helical antifreeze protein

The possible interaction models for an antifreeze protein from Tenebrio molitar (TmAFP) have been systematically studied using the methods of molecular mechanics, molecular dynamics and quantum chemistry. It is hoped that these approaches would provide insights into the nature of interaction between protein monomers through sampling a number of interaction possibilities and evaluating their interaction energies between two monomers in the course of recognition. The results derived from the molecular mechanics indicate that monomer's β-sheets would be involved in interaction area and the side chains on two β-faces can match each other at the two-dimensional level. The results from molecular mechanics and ONIOM methods show that the strongest interaction energy could be gained through the formation of H-bonds when the two β-sheets are involved in the interaction model. Furthermore, the calculation of DFT and analysis of van der Waals bond charge density confirm further that recognition between the two     

A Cell Solid Structure of cis-1,3-Cyclohexanedicarboxylic Acid and Its Complex Crystal with 4,4''''-Dipyridine

Carboxylic acids are important in crystal engineering because they can form strong and directional O-H…O hydrogen bonds as dimmer and catmer.[1] The dicarboxylic acids (not containing other hydrogen bonding groups) generally form the extended line structure interlinked through dimmer,[2] except that oxalic acid forms both the β-oxalic acid linked by dimmer (finite synthon) and the a-oxalic acid by catmer[3] (infinite synthon). A new molecular packing structure of cis-1,3-cyclohexanedicarboxylic acid (CHDA), which is different from line structure,[4] was gotten (P1/2, Figure 1). The novel structure has dimmer and catmer hydrogen bond pairs in the crystal and the hydrogen bond length of O-H…O is 0.268 nm in catmer and 0.264 nm in dimmer. The bond angles of O=C-O vary from 123.1° to 123.8° in catmer and from 123.1° to 122.0° in dimmer comparing with the ones in line structure.     

Computational studies of σ-type weak interactions between NCO/NCS radicals and XY(X = H,Cl;Y = F,Cl,and Br)

The triatomic radicals NCO and NCS are of interest in atmospheric chemistry,and both the ends of these radicals can potentially serve as electron donors during the formation of σ-type hydrogen/halogen bonds with electron acceptors XY(X = H,Cl;Y = F,Cl,and Br).The geometries of the weakly bonded systems NCO/NCS···XY were determined at the MP2/aug-cc-pVDZ level of calculation.The results obtained indicate that the geometries in which the hydrogen/halogen atom is bonded at the N atom are more stable than those where it is bonded at the O/S atom,and that it is the molecular electrostatic potential(MEP)-not the electronegativity-that determines the stability of the hydrogen/halogen bond.For the same electron donor(N or O/S) in the triatomic radical and the same X atom in XY,the bond strength decreases in the order Y = F > Cl > Br.In the hydrogen/halogen bond formation process for all of the complexes studied in this work,transfer of spin electron density from the electron donor to the electron acceptor is negligible,but spin density rearranges within the triatomic radicals,being transferred to the terminal atom not interacting with XY.     

Theory and algorithms for the excited states of large molecules and molecular aggregates

This project aims to attack the frontiers of electronic structure calculations on the excited states of large molecules and molecular aggregates by developing novel theoretical and computational methods. The methodology development is especially based on the time-dependent density functional theory (TDDFT) and valence bond (VB) theory, and is expected to be computationally effective and accurate as well. Research works on the following related subjects will be performed: (1) The analytical energy-derivative approaches for electronically excited state within TDDFT will be developed to reduce bypass the computational costs in the calculation of molecular excited-state properties. (2) The ab initio methods for electronically excited state based on VB theory and hybrid TDDFT-VB method will be developed to overcome the limitations of current TDDFT in simulating photophysics and photochemistry. (3) For larger aggregates, neither ab initio methods nor TDDFT is applicable. We intend to build the effective model Hamiltonian by developing novel theoretical and computational methods to calculate the involved microscopic physical parameters from the first-principles methods. The constructed effective Hamiltonian is then used to describe the excitonic states and excitonic dynamics of the natural or artificial photosynthesized systems, organic or inorganic photovoltaic cell. (4) The condensed phase environment is taken into account by combining the developed theories and algorithms based on TDDFT and VB with the polarizable continuum solvent models (PCM), molecular mechanism (MM), classical electrodynamics (ED) or molecular dynamics (MD) theory. (5) Highly efficient software packages will be designed and developed.     

CORRELATION BETWEEN GLASS TRANSITION OF POLYMERS AND ENERGY OF ROTATIONAL ISOMERIZATION OF MOLECULAR CHAINS

It has been shown that the free volume fraction at T_g is not a universal parameter for linear polymers of different molecular structure. The reason is that the volume expansion at T_g is partially contributed from the change of the numbers of conformations of isolated molecular chains due to internal rotation. In this paper, glassy transformation was connected with internal rotation of isolated molecular chains, and the relationship between free volume fraction of polymers at T_g and energy e of rotational isomerization of isolated molecular chains was formulated, e=-k·T_g·In (△α·T_g/1-△α. T_g). The values of calculated from the above formula are in good agreement with those published in the literatures. Thus, the method described in this paper can be used to estimate a parameter for the flexibility of isolated molecular chains.7     

Study on the Dynamics of Blending of Glucomannan with Carrageenan and Guaran Gum

In order to prove up the interaction between konjac glucomannan (KGM) and other amyloses, by using KGM, guaran gum and carrageenan as materials, their blending in different external conditions was modeled by means of molecular dynamics (MD) method. The result showed that 323 K was a significant turning point for the formation of hydrogen bond, and KGM and guaran gum were just juxtaposed together via intermolecular hydrogen bond; but with the addition of carrageenan, KGM, guaran gum and carrageenan were spirally twisted together, and when their blending proportion is 3:2:9 the combination was the most compact. Moreover, the research result has provided the sequent studies afterwards on amyloses with some references.     

Study of Two Puzzled Questions on the Fullerene C_（70）：A First-principles Study

The cycloaddition reactions of NH to different bonds on C70 have been studied by the first-principles calculations.The results indicate that the reactivity of cycloaddition reactions is determined by the directional curvature,KD,and the larger binding energy of Eb on the bond C5-C'5 can be ascribed to the unique bond which can be treated as the shortest bond of(5.5)-SWCNT in the four [6,6] ring fusion bonds.This work also discloses that the energy gap of different spin states is decided by the electronic density,and that of the frontier obitals for the bond C5-C'5 is larger than the value for the C4-C'4 bond.Furthermore,the transition state investigation of the two bond addition reactions provides a reaction barrier of 11.10 kcal/mol for the NH cycloaddition to the C5-C'5 bond;whereas,the addition reaction on C4-C'4 is a spontaneous pathway.Herein,the dynamics effect illustrates the [2+1] cycloaddition reaction on the equatorial C5-C'5 bond to be unfavorable.