Hydrogen bonded structure and dynamics of liquid-vapor interface of water-ammonia mixture: an ab initio molecular dynamics study

We have carried out ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and ammonia molecules. We have made a detailed analysis of the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and ammonia molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions of bulk and interfacial molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-ammonia hydrogen bonds at the interface with ammonia as the acceptor. The structure of the system is also investigated in terms of inter-atomic voids present in the system. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations.     

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C−N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a–2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C−N), which is why the six-membered ring lactams C−N bond are more rigid than those with five-membered ring lactams. The calculated ΔG^# values from the acylation reaction of the lactams (involving the S−H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C−N cleavage in the five-membered ring lactams especially in the 1–2 derivatives (17.58 kcal mol⁻¹). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.     

Competition between C-C and C-H Activation in Reactions of Neutral Nickel Atom with Cycloalkanes （n = 3-7）

A theoretical investigation of the reaction mechanisms for C-H and C-C bond activation processes in the reaction of Ni with cycloalkanes C,,H2. （n = 3-7） is carried out. For the Ni ＋ CnH2, （n = 3, 4） reactions, the major and minor reaction channels involve C-C and C-H bond activations, respectively, whereas Ni atom prefers the attacking of C-H bond over the C-C bond in CnH2n （n = 5=7）. The results are in good agreement with the experimental study. In all cases, intermediates and transition states along the reaction paths of interest are characterized, It is found that both the C-H and C-C bond activation processes are proposed to proceed in a one-step manner via one transition state. The overall C-H and C-C bond activation processes are exothermic and involve low energy barriers, thus transition metal atom Ni is a good mediator for the activity of cycloalkanes CnH2n （n = 3 -7）.     

Odd-even effects on the structure, stability, and phase transition of alkanethiol self-assembled monolayers

Molecular dynamics simulations were conducted to predict the structural properties and phase transition temperatures of n-alkanethiols CH(3)(CH(2))(n-1)SH (Cn, 4 ≤ n ≤ 22) self-assembled monolayers (SAMs) on Au (111) surfaces. We studied the effects of chain length on the structural properties, including tilt and orientation angles, and on phase transition temperature. We found clear dependence of the structural properties, on both the number of carbon atoms, n; and on n being odd or even. Alkanethiols with n ≤ 7 show liquid-like behavior and large rotational mobility, whereas those with n ≥ 12 are well-ordered and stable. For 12 ≤ n ≤ 15, odd-even effects are observed, where for n = odd, larger tilt angles, oriented in the direction of their next next nearest neighbor (NNNN), and for n = even, lower tilt angles, mostly tilted toward next nearest neighbor (NNN), were observed. For 15 ≤ n ≤ 19, we find tilt angle and orientation to be independent of n. For all alkanethiols, a gradual decrease of the tilt angle occurred by increasing the temperature from 300 to 420 K. Order-disorder phase transitions occurred at a certain temperature. This was signified by abrupt instabilities in the tilt orientation angle. This transition temperature showed an enhancement of ～67-100 °C over the melting point of the corresponding n-alkane bulk system. This enhancement depended on n, and was larger for n = odd. Overall, we found that odd alkanethiols show better structural and thermal stability, and smaller gauche defects.     

Rotational barriers of benzaldehydes in the framework of the intersecting-state model

A general intersecting-state model has been applied to the rotational barriers of benzaldehydes. It is found that 1n the gas phase the transition state bond order, n^#, 1s greater than 1.0, implying a siphoning of electronic density from the oxygen lone pairs into the transition state. In solution such siphoning is hindered due to the interactions of the oxygen lone pairs with the solvent molecules and n^# = 1.0. For protonated benzaldehydes rotation around a carbon-carbon double bond seems to occur and n^# = 1.0, which is in agreement with a bond breaking at the transition state. Substituent effects are studied and estimations of rotational energy barriers for several benzaldehydes in the vapour phase are presented.     

Pressure-induced isostructural phase transition and correlation of FeAs coordination with the superconducting properties of 111-type Na(1-x)FeAs

The effect of pressure on the crystalline structure and superconducting transition temperature (T(c)) of the 111-type Na(1-x)FeAs system using in situ high-pressure synchrotron X-ray powder diffraction and diamond anvil cell techniques is studied. A pressure-induced tetragonal to tetragonal isostructural phase transition was found. The systematic evolution of the FeAs(4) tetrahedron as a function of pressure based on Rietveld refinements on the powder X-ray diffraction patterns was obtained. The nonmonotonic T(c)(P) behavior of Na(1-x)FeAs is found to correlate with the anomalies of the distance between the anion (As) and the iron layer as well as the bond angle of As-Fe-As for the two tetragonal phases. This behavior provides the key structural information in understanding the origin of the pressure dependence of T(c) for 111-type iron pnictide superconductors. A pressure-induced structural phase transition is also observed at 20 GPa.     

Phase transition of a single star polymer: a Wang-Landau sampling study

Star polymers, as an important class of nonlinear macromolecules, process special thermodynamic properties for the existence of a common connecting point. The thermodynamic transitions of a single star polymer are systematically studied with the bond fluctuation model using Wang-Landau sampling techniques. A new analysis method employing the shape factor is proposed to locate the coil-globule (CG) and liquid-crystal (LC) transitions, which shows a higher efficiency and accuracy than the canonical specific heat function. The LC transition temperature is found to obey the identical scaling law as the linear polymers. However, the CG transition temperature shifts towards the LC transition with the increasing of the arm number. The reason is that for the star polymer a lower temperature is needed for the attractive force to overcome the excluded volume effect of the polymer chain because of its high arm density. This work clearly proves the structural distinction of the linear and star polymers can only affect the CG transition while has no influence on the LC transition.     

Lead-free thermochromic perovskites with tunable transition temperatures for smart window applications

The structural flexibility of hybrid perovskite materials allows for phase transition and consequently thermochromic properties.Here we investigate the thermochromic performance in a series of copper-based layered perovskites with organic cations having different alky chain lengths. Their transition temperature is found to be dependent on the organic cations due to molecular motion and hydrogen bond interaction, providing possibilities to prepare thermochromic semiconductors near room temperature for smart window applications.     

Electronic effects in (salen)Mn-based epoxidation catalysts

Presented are density functional calculations on various Mn(salen) systems that are active catalysts in the epoxidation of olefins. Correlation of various structural properties such as Mn=O bond strengths, atomic charges, and C-O distances of evolving bonds in transition state geometries with modified Hammett constants reveal a mechanistic picture of the epoxidation reaction, supporting previous experimental results. Enantioselectivity is tied to the position of a transition state along the reaction coordinate for the first C-O bond formation step, when an olefin is approaching the epoxidation catalyst. Electronic effects exhibited by the 5,5' substituents of the salen ligand manifest themselves in a tuning of the Mn=O bond strength, which in turn influences the C-O distance of the forming bond in the transition state geometry.     

Core ionization energies of atoms and ions calculated using the generalized Sturmian method

The physical event of the umbrella inversion of ammonia has been studied in detail by application of the formalisms of frontier orbital theory, the density functional theory, the localized molecular orbital method, and the energy partitioning analysis. An intuitive structure for the transition state and dynamics of the physical process of structural reorganization prior to inversion have been suggested. The computation starts with the CNDO/2 equilibrium geometry, and thereafter the cycle proceeds through all the conformations of ammonia obtained by varying the ∠HNH angle in steps of 2° from its equilibrium value up to the transition state. The geometry of each conformation is optimized with respect to the length of the N–H bond. The glimpses of the charge density reorganization during the movement of the molecule from equilibrium conformation toward the transition state is computed in terms of dipole moment and the quantum mechanical hybridizations of bond pair and lone pair of N atom through the localized molecular orbitals (LMOs) of all the conformations. Results demonstrate that as the geometry of the molecule begins to evolve through the reorganization of structure, the N–H bond length and the dipole moment begin to decrease, and the trend continues up to the transition state. The dipole moment of the molecule at the suggested transition state is zero. The computed nature of quantum mechanical hybridization of bond pair and lone pair of the N atom as a function of reaction coordinates of the ∠HNH angles reveals that the percentage of s character of the lone pair hybrid decreases and that of the bond pair hybrid forming the σ(N–H) bond increases during the process of geometry reorganization from the equilibrium shape to the transition state. The rationale of the zero dipole moment of the transition state for inversion is not straightforward from its point‐group symmetry, but is self‐evident from its electronic structure drawn in terms of LMOs. The electronic structure of the transition state, which may be drawn in terms of the LMOs, seems to closely reproduce its suggested intuitive structure. The pattern of variation of dipole moment and nature of the changes of the percentage of the s character in the lone pair hybrid creating dipole with the evolution of geometry during the physical process of structural reorganization for the inversion are found to be nicely correlated according to the suggestion of Coulson. The profiles of the increasing strength of the N–H bond and the increasing percentage of s character of the bond pair hybrid of N atom forming this bond as a function of reaction coordinates are also found to be correlated in accordance with the suggestion of Coulson. The profile of global hardness as a function of reaction coordinate seems to demonstrate that the dynamics of the evolution of the molecular structure from equilibrium shape to the transition state following the course of suggested mode of structural reorganization conforms to the principle of maximum hardness (PMH). The profiles of parameters like the energies of highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO), the gap in energy between HOMO and LUMO, the global hardness, the global softness, and chemical potential as a function of reaction coodinates of a continuous structural evolution from equilibrium shape to the transition state mimic the potential energy diagram of the total energy. Both the frontier orbital parameters and the density functional quantities are found to be equally effective and reliable to monitor the process of necessary structural reorganization prior to the inversion of mofecules. An energy partitioning analysis demonstrates that the origin of barrier has no unique single source rather as many as four mutually exclusive but interacting one‐ and two‐center energy terms within the molecule entail the origin and the height of the barrier. From a close analysis of the results, it seems highly probable that the necessary structural reorganization prior to umbrella inversion of ammonia most realistically occurs following the course of normal modes of vibration of the molecule. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 1–26, 2000     

Topological studies on IRC paths of the isomerization reaction of silicon methyl-nitrene

On the basis of kinetic study of isomerization reaction of H_3Si-N, ab initio (RHF, UHF/6-31G) calculations on some points of the singlet and triplet reaction paths were carried out. The breakage and formation of chemical bond in the reaction are discussed. The calculated results show that there is a transitional structure of three-membered ring on each of reaction paths. A 'structural transition region' and a 'structural transition state' in both of studied reaction are found. Our previous conclusion that the structure transition state (STS) always appears before the energy transition state (ETS) in endothermic reaction and after ETS in exothermic reaction is further confirmed. The relationship between the change of spin density distribution and the structural transition state are investigated.     

Understanding the dependence of the transitional properties of liquid crystal dimers on their molecular geometry

The characteristic feature of liquid crystal dimers, in which two mesogenic groups are linked by a flexible spacer, is often thought to be the strong odd-even effect exhibited by their transitional properties. That is, the nematic-isotropic transition temperature and the entropy of transition are large for dimers with an even number of groups in the spacer in comparison with those for neighbouring dimers with an odd number of groups. However, the magnitude of the odd-even effect along a homologous series of dimers is found to depend strongly on the nature of the link between the mesogenic group and the spacer. This dependence is thought to originate in the variation of the molecular geometry with the linking group, a view which is supported by detailed molecular field theory calculations involving all of the conformational states. Here we are concerned with developing a more transparent understanding of this geometrical effect using a simple model of the dimers in which all of the conformational states are replaced by just two, a linear and a bent conformer. The model has been found to exhibit a strong odd-even effect as well as a nematic-nematic transition when the bond angle is tetrahedral. We have used this model to explore the dependence of the transitional properties of liquid crystal dimers on their geometry by varying the bond angle of the bent conformer. The behaviour predicted by the model for the nematic-isotropic transition is found to be in qualitative agreement with experiment. In addition, the nematic-nematic transition is observed to exhibit a critical behaviour as the bond angle is increased. At the other extreme, when the bond angle is reduced to its limiting value of 90° there is a very strong first order transition between a discotic and a calamitic nematic.     

聚合物屈服中结构变化的计算机模拟

用分子模拟方法对近来关于在屈服中是否存在结构改变的问题进行了考察.结果表明,在屈服附近键长与键角没有明显的变化,而且分子间相互作用主宰着屈服过程.研究发现,屈服过程中有一个“原子跳跃”的结构转变现象,即部分原子的位移超出所有原子平均位移的10倍以上.另外,高分子链间堆砌的复杂性引起屈服点附近的多重原子跳跃发生.用该结果可以较合理地解释高分子有一个宽的屈服峰.     

Techniques for the calculation of three-dimensional structural similarity using inter-atomic distances

Summary This paper reports a comparison of several methods for measuring the degree of similarity between pairs of 3-D chemical structures that are represented by inter-atomic distance matrices. The methods that have been tested use the distance information in very different ways and have very different computational requirements. Experiments with 10 small datasets, for which both structural and biological activity data are available, suggest that the most cost-effective technique is based on a mapping procedure that tries to match pairs of atoms, one from each of the molecules that are being compared, that have neighbouring atoms at approximately the same distances.     

Structure, vibrational spectra, and unimolecular dissociation of gaseous 1-fluoro-1-phenethyl cations

The multiple CF bond character of PhCFMe (+) ions has been examined by means of theory, vibrational spectroscopy of the gaseous ions, and unimolecular decomposition chemistry. Atoms in Molecules analysis of DFT wave functions gives a CF bond order of n = 1.25 (as compared with n = 1.38 for Me 2CF (+), relative to n = 1 for fluoromethane and n = 2 for diatomic CF (+)), which is consistent with calculations of adiabatic CF stretching frequencies (nu CF). Experimental gas phase IR spectra, recorded by means of resonant multiphoton dissociation (IRMPD) using a free-electron laser connected to an FTICR mass spectrometer, show good agreement with predicted band positions for five deuterated isotopomers of PhCFMe (+). Metastable ion decompositions of deuterated analogues of PhCFMe (+) show the same HF/DF loss patterns as those produced by IRMPD. The evidence supports the conclusion that PhCFMe ions retain structural integrity until they become sufficiently excited to dissociate, whereupon they undergo intramolecular hydrogen scrambling that is competitive with HF/DF expulsion. Relative rates of hydrogen transposition and unimolecular dissociation are extracted from relative experimental fragment ion abundances. The predominant decomposition pathway is inferred to operate via a five-center transition state, as opposed to a four-center transition state for HF loss from gaseous Me 2CF (+).     

Structural measures of element-oxygen bond covalency from the changes to the delocalisation of the carboxylate ligand

The data set of more than 40,000 crystal structures containing the carboxylate group that have been deposited in the CSD has been used to examine the structural changes that occur in the carboxylate C-O bond lengths upon binding to different elemental centres. We report here quantifiable structural changes that are dependent on the elemental centre with which the group is interacting. For the main-group elements the trends are entirely periodic and follow those traditionally associated with covalency; elements exhibiting electronegativity closest to that of oxygen exhibit the largest structural change. In addition, we find the measure is extendable to both the transition metals and the lanthanoids and actinoids. Amongst the transition metals the trends of Pauling neutrality are not only maintained, but are quantifiable. The difference between the two C-O bond lengths increases with oxidation state and decreases with an increase in coordination number. All of the lanthanoids exhibit covalency within error of each other and the bonds to the actinoids are found to be more covalent than those to the lanthanoids. From the data analysis we are able to derive a correlation between the lengths of the two carboxylate arms that allows us to quantify percentage covalent character defined in terms of the resonance contributions to the carboxylate group.     

应用ABEEM/MM模型研究水分子团簇(H2O)n (n=11～16)的性质

应用ABEEM/MM 模型计算了较大的水分子团簇(H2O)n (n=11~16)的各种性质,如：优化的几何构型, 氢键个数, 结合能, 稳定性, ABEEM 电荷分布, 偶极矩, 以及结构参数、平均氢键个数和强度, 增加的团簇结合能等.结果表明,从立方体结构到笼状结构的过渡出现在n=12的水分子团簇中,随着类似于笼状结构特点的不断增强,五元环的富集程度有所增加.     

Ab initio studies on Al(+)(H(2)O)(n), HAlOH(+)(H(2)O)(n-1), and the size-dependent H(2) elimination reaction

We report computational studies on Al(+)(H(2)O)(n), and HAlOH(+)(H(2)O)(n-1), n = 6-14, by the density functional theory based ab initio molecular dynamics method, employing a planewave basis set with pseudopotentials, and also by conventional methods with Gaussian basis sets. The mechanism for the intracluster H(2) elimination reaction is explored. First, a new size-dependent insertion reaction for the transformation of Al(+)(H(2)O)(n), into HAlOH(+)(H(2)O)(n-1) is discovered for n > or = 8. This is because of the presence of a fairly stable six-water-ring structure in Al(+)(H(2)O)(n) with 12 members, including the Al(+). This structure promotes acidic dissociation and, for n > or = 8, leads to the insertion reaction. Gaussian based BPW91 and MP2 calculations with 6-31G* and 6-31G** basis sets confirmed the existence of such structures and located the transition structures for the insertion reaction. The calculated transition barrier is 10.0 kcal/mol for n = 9 and 7.1 kcal/mol for n = 8 at the MP2/6-31G** level, with zero-point energy corrections. Second, the experimentally observed size-dependent H(2) elimination reaction is related to the conformation of HAlOH(+)(H(2)O)(n-1), instead of Al(+)(H(2)O)(n). As n increases from 6 to 14, the structure of the HAlOH(+)(H(2)O)(n-1) cluster changes into a caged structure, with the Al-H bond buried inside, and protons produced in acidic dissociation could then travel through the H(2)O network to the vicinity of the Al-H bond and react with the hydride H to produce H(2). The structural transformation is completed at n = 13, coincident approximately with the onset of the H(2) elimination reaction. From constrained ab initio MD simulations, we estimated the free energy barrier for the H(2) elimination reaction to be 0.7 eV (16 kcal/mol) at n = 13, 1.5 eV (35 kcal/mol) at n = 12, and 4.5 eV (100 kcal/mol) at n = 8. The existence of transition structures for the H(2) elimination has also been verified by ab initio calculations at the MP2/6-31G** level. Finally, the switch-off of the H(2) elimination for n > 24 is explored and attributed to the diffusion of protons through enlarged hydrogen bonded H(2)O networks, which reduces the probability of finding a proton near the Al-H bond.     

Steering Site-Selectivity in Transition Metal-Catalyzed C−H Bond Functionalization: the Challenge of Benzanilides

Selective C−H bond functionalization catalyzed by metal complexes have completely revolutionized the way in which chemical synthesis is conceived nowadays. Typically, the reactivity of a transition metal catalyst is the key to control the site-, regio- and/or stereo-selectivity of a C−H bond functionalization. Of particular interests are molecules that contain multiple C−H bonds prone to undergo C−H bond activations with very similar bond dissociation energies at different positions. This is the case of benzanilides, relevant chemical motifs that are found in many useful fine chemicals, in which two C−H sites are present in chemically different aromatic fragments. In the last years, it has been found that depending on the metal catalyst and the reaction conditions, the amide motif might behave as a directing group towards the metal-catalyzed C−H bond activation in the benzamide site or in the anilide site. The impact and the consequences of such subtle control of site-selectivity are herein reviewed with important applications in carbon-carbon and carbon-heteroatom bond forming processes. The mechanisms unraveling these unique transformations are discussed in order to provide a better understanding for future developments in the field of site-selective C−H bond functionalization with transition metal catalysts.     

The origin of diastereofacial control in allylboration reactions using tartrate ester derived allylboronates: attractive interactions between the Lewis acid coordinated aldehyde carbonyl group and an ester carbonyl oxygen

Transition-state structures for the allylboration reaction between the tartrate ester and tartramide modified allylboronates and acetaldehyde are located at the B3LYP/6-31G* level of theory. An attractive interaction between the boron-activated aldehyde and the ester or amide carbonyl oxygen lone pair is found to play a major role in the favored transition states 11a and 13. This attractive interaction appears to be electrostatic in origin. However, an n --> pi* charge-transfer type of interaction has not been ruled out. The distance (2.77 A) between the aldehydic hydrogen and the carbonyl oxygen in transition state 13 is beyond the sum of van der Waals radii. The formyl C-H...O bond angle (109 degrees) in this transition structure deviates far from linearity. Therefore, hydrogen-bonding interactions between the formyl C-H and the amide carbonyl oxygen are considered negligible. The distance (3.81 A) between the aldehydic oxygen and the amide carbonyl oxygen in the diastereomeric, disfavored transition state 14 is also beyond the van der Waals radii, which suggests that n/n electronic repulsion plays a lesser role in stereodifferentiation in the allylboration reaction than originally proposed.