On the directed gas phase synthesis of the imidoborane molecule (HNBH)--an isoelectronic molecule of acetylene (HCCH)

The elementary reaction of ground state boron atoms, (B((2)P(j))), with ammonia (NH(3)(X(1)A(1))) was conducted under single collision conditions at a collision energy of 20.5 ± 0.4 kJ mol(-1) in a crossed molecular beams machine. Combined with electronic structure calculations, our experimental results suggested that the reaction was initiated by a barrier-less addition of the boron atom to the nonbonding electron pair of the nitrogen atom forming a weakly bound BNH(3) collision complex. This intermediate underwent a hydrogen shift to a doublet HBNH(2) radical that decomposed via atomic hydrogen loss to at least the imidoborane (HBNH(X(1)Σ(+)) molecule, an isoelectronic species of acetylene (HCCH(X(1)Σ(g)(+))). Our studies are also discussed in light of the isoelectronic C(2)H(3) potential energy surface accessed via the isoelectronic carbon-methyl system.     

Polarization and bonding of the intrinsic characteristic contours of hydrogen and fluorine atoms of forming a hydrogen fluoride molecule based on an ab initio study

The spatial changing feature of the shapes and sizes of the system consisted of one hydrogen atom and one fluorine atom of forming a hydrogen fluoride molecule is investigated. We give formalism of the potential acting on an electron in a molecule and derive its concrete expression in Hartree-Fock self-consistent molecular orbital theory including configuration interaction. The program of calculating the potential acting on an electron in a molecule is programmed and compiled in the framework of the MELD program package. We formulate briefly the approach of the molecular intrinsic characteristic contour (MICC) which is defined in terms of the classical turning points of electronic motion. The MICC for a molecular system is intrinsic and can be calculated by means of an ab initio CI method. Then, the polarization and bonding features of the intrinsic characteristic contours of hydrogen and fluorine atoms forming a hydrogen fluoride molecule are presented and discussed from ab initio calculations. Furthermore, electron density distribution as an added dimension has been demonstrated on the changing MICC and thus the vivid polarization and bonding features for a chemical process have been shown. It seems that at the early stage (internuclear distance Ind=5.0-20.0 a.u.) the fluorine atom gives more enthusiastic with the sensitive and expanded polarization to welcome coupling with the hydrogen atom while the latter has little response even "shy" with shrinking a bit its size at the beginning of putting the two atoms into a system and it is only around the critical point, the contact point (Ind=4.73 a.u.), that both of them stretch their hands and arms to meet and then fuse together.     

Rydberg atom mediated polar molecule interactions: a tool for molecular-state conditional quantum gates and individual addressability

We study the possibility to use interaction between a polar molecule in the ground electronic and vibrational state and a Rydberg atom to construct two-qubit gates between molecular qubits and to coherently control molecular states. A polar molecule within the electron orbit in a Rydberg atom can either shift the Rydberg state, or form a Rydberg molecule. Both the atomic shift and the Rydberg molecule states depend on the initial internal state of the polar molecule, resulting in molecular state dependent van der Waals or dipole-dipole interaction between Rydberg atoms. Rydberg atoms mediated interaction between polar molecules can be enhanced up to 10(3) times. We describe how the coupling between a polar molecule and a Rydberg atom can be applied to coherently control molecular states, and specifically, to individually address molecules in an optical lattice, and to non-destructively readout molecular qubits.     

Trajectory calculation results on the orientation of a diatomic molecule in collision with an atom

Orientational effects in collisions between a diatomic molecule and a noble gas atom are studied by classical trajectory calculations. A preferable ”perpendicular orientation“ of the molecule is found at the moment of closest approach of the atom. This orientational effect is more pronounced in collisions with heavy atoms.     

Geometric structure of a molecule of Epitalon tetrapeptide: A molecular-dynamics simulation

Variation of the geometric parameters of a molecule of Epitalon tetrapeptide (Ala-Glu-Asp-Gly) over a period of 1500 ps was simulated by the method of molecular dynamics using AMBER force field. The structure of the molecule is stabilized by two salt bridges formed by the N-terminal nitrogen atom and oxygen atoms of Asp and Glu side chains. The biological effect of Epitalon was attributed to formation of salt or hydrogen bonds involving one or several ionizable functional groups of the molecules.     

Effective polarizability of a molecule physisorbed on a spherical metal particle: nonlocal effects

The electromagnetic interactions between a molecule and a spherical metal particle affect the linear response of the molecule. We present a general method to calculate the effective dynamic polarizability of such physisorbed systems by including the nonlocal character of the electron response in the sphere. Our model takes into account several long-range mechanisms connected to the dispersion, induction and local field effects. When the sphere reduces to a single atom, we recover results already known for a pair of atoms.     

Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia

The hydrogen bond arrangement in a complex of cellulose with ammonia has been studied using neutron crystallography in combination with molecular dynamics simulations. The O6 atom of the hydroxymethyl group is donor in a highly occupied hydrogen bond to an ammonia molecule. This rotating ammonia molecule is donor in partially occupied and transient hydrogen bonds to the O2, O3 and O6 atoms of the hydroxyl groups of other chains. The hydrogen atom bound to the O3 atom is disordered but it is almost always involved in some type of hydrogen bonding. It is donated in a hydrogen bond most of the time to the O5 atom on the same chain. However, it also rotates away from this O5 atom to be donated to an ammonia molecule part of the time. On the other hand the hydrogen atom bound to the O2 atom is free from hydrogen bonding most of the time. It is donated in a hydrogen bond to the O6 atom on a neighboring chain only with a relatively small probability. These results provide new insights into how hydrogen bonds are rearranged during the conversion of cellulose I to cellulose III_I by ammonia treatment.     

Trapped water molecule in the charge separation of a bacterial reaction center

Low-frequency oscillations in the absorption spectrum at 1020 nm, connected to the primary charge separation process in Rhodobacter sphaeroides, have been shown by Yakovlev et al. to be caused by rotational motion of an interstitial water molecule called "water-A". The same water molecule was shown by Potter et al. to increase the rate of charge separation by a factor of 8. We have carried out geometry optimization of water-A and its nearest atoms in the protein pocket, using density functional theory (DFT). There are strong hydrogen bonds to the axial imidazol group of the B part of the special pair (P=PAPB) and to the keto carbonyl group of ring V of the accessory chlorophyll (BA). Rotation of water-A is thus impossible in the electronic ground state. We have tried to support our speculations on other possible mechanisms by calculations. The P(+)BA(-) charge transfer state is stabilized by proton transfer from water-A and simultaneous proton transfer from the axial group of PB to water-A. After double proton transfer the hydrogen bond to the keto group disappears whereby a possibility opens up for almost free water rotation. The results therefore would explain the 32 cm(-1) oscillation of Yakovlev et al. The proposed mechanism assumes, however, that the general assumption that the activation energy disappears in the primary charge separation of bacterial photosynthesis, holds also for this special case.     

Coordination polymer of lanthanum: synthesis,properties and crystal structure of [La(4,4′-bipyridine)(CCl2HCOO)3(H2O)] n

A new mixed ligand complex of general formula [La(H₂O)(4,4′-bpy)(CCl₂HCOO)₃] _n has been synthesized and characterized by elemental and thermal analysis, IR spectroscopy and conductivity studies. The crystal and molecular structure was determined. The lanthanum atom is ten coordinate by four oxygen atoms from two chelating tridentate dichloroacetate substituents, two oxygen atoms from two bidentate bridging dichloroacetate groups, two oxygen atoms from two bridging tridentate dichloroacetate substituent, one oxygen atom of water molecule and one nitrogen atom from 4,4′-bipyridyl substituent. The coordination polyhedron of central atom can be described as tetradecahedron. The molecules are built up by O–H?···?N hydrogen bonds to a two-dimensional network.     

Ab initio molecular dynamics study of H2 formation inside POSS compounds

The mechanism and dynamics of the formation of a hydrogen molecule by incorporating two hydrogen atoms in a stepwise manner into the cavity of some POSS (polyhedral oligomeric silsesquioxanes) compounds has been investigated by ab initio molecular orbital and ab initio molecular dynamics (AIMD) methods. The host molecules in the present reactions are two types of POSS, T(8) ([HSiO(1.5)](8)) and T(12)(D(2d)) ([HSiO(1.5)](12)). AIMD simulations were performed at the CASSCF level of theory, in which two electrons and two orbitals of the colliding hydrogen atoms are included in the active space. The trajectories were started by inserting the second hydrogen atom into the hydrogen atom-encapsulated-POSS (H + H@T(n) → H(2)@T(n); n = 8 and 12). In many cases, the gradual formation of a hydrogen molecule has been observed after frequent collisions of two hydrogen atoms within the cages. The effect of the introduction of an argon atom in T(12) is discussed as well.     

Potential energy surfaces for the interaction of atomic and diatomic hydrogen with lithium metal clusters

In this paper a modified CNDO/2 method is used to study the interaction of hydrogen atoms and molecules with molecular clusters simulating the (100) surface of solid lithium metal. The modification, described in an earlier papers, involves rescaling bicentric CNDO/2 energy contributions with known diatomic bond energies. Potential energy curves are calculated for six attack points by the hydrogen atom on the surface, and for one attack point by the molecule. The results indicate that in both atom and molecule forms hydrogen penetrates the surface and that the molecule most likely dissociates.     

The mass spectrum of isopropyl o-toluate

The formation of an [M + 1]⁺ ion and the fragmentation of isopropyl o-toluate have been investigated by the deuterium labelling technique and kinetic energy release measurements. The hydrogen atom involved in the [M + 1]⁺ ion formation does not originate from a specific part of the molecule, but from all parts. A small amount of hydrogen exchange between the secondary carbon atom in the isopropyl group and the carbon atoms in the tolyl group takes place prior to decomposition of the molecular ion into the m/z 136 ion by a McLafferty rearrangement. Either almost complete scrambling of the hydroxyl hydrogen atom and the methyl hydrogen atoms in tolyl group or an almost equilibrated exchange of the hydroxyl hydrogen atom with one of the remaining hydrogen atoms in tolyl group also takes place prior to the elimination of a water molecule from the intermediate m/z 136 ion.     

Ab initio multireference configuration-interaction study of hydrogen molecule activation by Cs-promoted Pt clusters

The adsorption of the H2 molecule on CsnPt(5-n) bcc (111) clusters for Cs/Pt rates of 20%, 40%, and 80% is studied using ab initio multiconfigurational self-consistent field plus multireference configuration-interaction variational and perturbative calculations. The H2 interaction with the clusters is studied in ground and excited states with geometry optimization, where the hydrogen adsorption takes place by a Pt atom. These calculations are compared with those of H2 adsorption on Pt4. The most stable configurations of Cs/Pt4 and Cs2Pt3 clusters (Cs/Pt rates of 20% and 40%) are a doublet and a closed-shell singlet, respectively. Both clusters capture and activate the hydrogen molecule and their behaviors resemble Pt4. The H2 capture distances are, respectively, similar and smaller than Pt4 capture distances, while the H-H bond dissociation distances are similar and bigger than those of Pt4; however, none of them presents activation barriers. The most stable Cs4Pt cluster (Cs/Pt rate of 80%) is also a closed-shell singlet; it also captures and activates the hydrogen molecule and shows a different behavior as compared with Cs/Pt4, Cs2Pt3, and Pt4 clusters. The capture distance is quite smaller and is obtained after surmounting an activation barrier. For all clusters studied here, no hydrogen absorption was observed, only the adsorption of H2.     

Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O · HO)

The hydrogen bonding complexes formed between the H₂O and OH radical have been completely investigated for the first time in this study using density functional theory (DFT). A larger basis set 6‐311++G(2d,2p) has been employed in conjunction with a hybrid density functional method, namely, UB3LYP/6‐311++G(2d,2p). The two degenerate components of the OH radical ²Π ground electronic state give rise to independent states upon interaction with the water molecule, with hydrogen bonding occurring between the oxygen atom of H₂O and the hydrogen atom of the OH radical. Another hydrogen bond occurs between one of the H atoms of H₂O and the O atom of the OH radical. The extensive calculation reveals that there is still more hydrogen bonding form found first in this investigation, in which two or three hydrogen bonds occur at the same time. The optimized geometry parameter and interaction energy for various isomers at the present level of theory was estimated. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. The estimates of the H₂O · OH complex's vibrational modes and predicted IR spectra for these structures are also made. It should be noted that a total of 10 stationary points have been confirmed to be genuine minima and transition states on the potential energy hypersurface of the H₂O · HO system. Among them, four genuine minima were located. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

第一性原理模拟氢气分子在氧化硅团簇上的吸附

基于密度泛函理论,采用广义梯度近似(GGA)分析了H2分子吸附在氧化硅团簇上的几何结构、电子性质以及吸附能.结果发现:H2分子与Si3O4团簇相互作用时,H2分子被分解,游离的H原子优先吸附在末端Si原子上,表明Si3O4团簇体系对氢气的存储主要依赖于末端存在悬挂键的Si原子,接着H2分子才以分子的形式以较小吸附能吸附在Si3O4H4团簇上.氢气分子主要引起与其邻近的原子电荷的重新分布.该团簇体系的红外、拉曼光谱图有效地鉴定了H2分子的吸附状态,为理论上确定团簇的稳定结构和实验上对观测结果的分析提供有力的途径.     

Enhancement of hydrogen physisorption on graphene and carbon nanotubes by Li doping

Density-functional calculations of the adsorption of molecular hydrogen on a planar graphene layer and on the external surface of a (4,4) carbon nanotube, undoped and doped with lithium, have been carried out. Hydrogen molecules are physisorbed on pure graphene and on the nanotube with binding energies about 80-90 meV/molecule. However, the binding energies increase to 160-180 meV/molecule for many adsorption configurations of the molecule near a Li atom in the doped systems. A charge-density analysis shows that the origin of the increase in binding energy is the electronic charge transfer from the Li atom to graphene and the nanotube. The results support and explain qualitatively the enhancement of the hydrogen storage capacity observed in some experiments of hydrogen adsorption on carbon nanotubes doped with alkali atoms.     

Definitive evidence for the contribution of biradical character in a closed-shell molecule, derivative of 1,4-bis-(4,5-diphenylimidazol-2-ylidene)cyclohexa-2,5-diene

This study provides conclusive proof that the thermally excited open-shell state with biradical character is contributing to the ground state of a closed-shell molecule, tF-BDPI-2Y, where four hydrogen atoms at the central phenylene ring are substituted with four fluorine atoms of 1,4-bis-(4,5-diphenylimidazol-2-ylidene)cyclohexa-2,5-diene (BDPI-2Y). A small increase in the population of biradical species of tF-BDPI-2Y results in the formation of the dimer form by the radical recombination reaction. Controlling the equilibrium between a closed-shell diamagnetic-quinoid state and an open-shell paramagnetic-biradical state will provide significant progress in the field of pi-conjugated delocalized biradical chemistry.     

The interaction of nitrogen and carbon monoxide with certain ions and neutral species

MNDO method is used to study the interaction of nitrogen and carbon monoxide molecules with a proton, hydrogen atom, hydride ion, hydrogen molecule ion and hydrogen molecule. Predicted geometries and heats of reaction of different complexes are presented. The wave functions are analyzed in terms of ground state charge distributions and overlap populations. Electronic effects accompanying complexation are also discussed.     

Hydrogen-bond interactions in hydrated 6-selenoguanine tautomers: a theoretical study

A comprehensive theoretical investigation has been performed to study the six most stable complexes of isolated, mono, and hexahydrated 6-selenoguanine tautomers. The ground state geometries are studied at the density-functional theory and Møller–Plesset Perturbation theory implementing the 6-311++G (2d, 2p) basis set. The intermolecular distances between the water molecule and the acceptor atom of 6-selenoguanine is about 0.6 Å longer for hydrogen bonds involving selenium atom. The relative Gibbs free energy of the 6-selenoguanine tautomers favors the selenone tautomer. The majority of the stable monohydrated complexes are the one in which the oxygen atom of water accepts the acidic N7-H proton while donating a proton to the carbonyl selenium atom of 6-selenoguanine; the interaction toward N7-H being stronger than that with the selenium site. The amino group planarity has been found to be increased in the hydrated complexes. The examination of molecular orbital reveals a moderate band gap between the donor and acceptor atoms of isolated and hydrated complexes. An excellent linear correlation is found to exist between electron density and laplacian of electron density with hydrogen-bond length through atoms in molecule analysis. The natural bond orbital analysis shows a maximum charge transfer of 0.060e for selenium acceptors and around 0.025e for selenium donors.     

Water inside a hydrophobic cavitand molecule

The structure and dynamics of water inside a water-soluble, bowl-shaped cavitand molecule with a hydrophobic interior are studied using molecular dynamics computer simulations. The simulations find that the number of inside water molecules is about 4.5, but it fluctuates from being completely empty to full on a time scale of tens of nanoseconds. The transition from empty to full is energetically favorable and entropically unfavorable. The water molecules inside have fewer hydrogen bonds than the bulk and in general weaker interactions; the lower energy results from the nearest-neighbor interactions with the cavitand atoms and the water molecules at the entrance of the cavitand, interactions that are lost upon dewetting. An analysis of translational and rotational motion suggests that the lower entropy of the inside water molecules is due to decreased translational entropy, which outweighs an increased orientational entropy. The cavitand molecule acts as a host binding hydrophobic guests, and dewetting can be induced by the presence of a hydrophobic guest molecule about 3 A above the entrance. At this position, the guest displaces the water molecules which stabilize the inside water molecules and the empty cavitand becomes more stable than the full.