Research

Computational Material

First Principles Molecular Dynamics Study of Filled Ice Hydrogen Hydrate

Ohki Kambara,  Kaito Takahashi, Michitoshi Hayashi and Jer-Lai Kuo Phys. Chem. Chem. Phys. 14, 11484 (2012) link

We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C2 by using first principles molecular dynamics simulation. It was found that the experimentally reported “cubic” structure is unstable at low temperature and/or high pressure: The “cubic” structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the “cubic” symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in “cubic” symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules’ rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures.

FIG.1 Four schematic models of structure. (a) Space group P41212; (b) space group Pna21; (c) space group I41/amd. H atoms of H2O have half occupation indicating the hydrogen bond disordered network; (d) space group Fd-3m. H atoms of H2O have half occupation. The rotating guest H2 molecules are represented by a light blue sphere; the red balls represent oxygen atoms in water molecules, the yellow balls indicate hydrogen atoms in water molecules, the grey balls indicate the hydrogen atoms of the hydrogen molecules.

Calculation of near K edge x-ray absorption spectra and hydrogen bond network in ice XIII under compression

Jingyun Zhang, Zhi-Ren Xiao, and Jer-Lai Kuo, J. Chem. Phys. 132, 184506 (2010) link

The hydrogen bond network, oxygen K edge x-ray absorption spectra (XAS), and electronic structure of ice XIII under compression have been extensively studied by density functional theory (DFT). We showed that DFT methods yield a ground state consistent with previous neutron scattering experiment and a few low-enthalpy metastable states are likely to coexist from the total enthalpy calculations. Oxygen K edge XAS of four low-enthalpy configurations was studied with the aim to shed light on the local structure in these configurations. We demonstrated that pre-edge of oxygen K edge XAS is a common feature appearing in all these four structures while major spectral differences exist in the main peak area. Therefore, we arrived at the conclusion that the main peak is more sensitive to the local hydrogen bond environment and could be used as an effective tool to distinguish these four configurations. We also found that the pre-edge has main contribution from O 1s-4a1 transitions and its intensity was suppressed by pressure while the main peak is mostly coming from O 1s-2b2 transitions. 

FIG. 2. Four predicted lowest enthalpy structures in which .a. is equivalent to the experimental structure in Ref. 1. The red and white balls represent oxygen and hydrogen atoms, respectively, and the light blue dashed lines represent hydrogen bonds.

FIG. 3. Calculated oxygen K edge XAS of the corresponding four structures given in Fig. 2 with standard deviation obtained by averaging over all distinct oxygen sites.

Quantum Chemical Investigation of Trends in the Electronic and Geometric Properties of Two-Dimensional Materials 

We are interested in understanding the structural and electronic properties of two-dimensional materials like transition metal dihalides and transition metal dichalcogenides. Due to the large variety of possible combinations of metal and anion, the potentially possible structures form a class of materials with rather inhomogeneous properties. One objective of our study is to identify the trends in the material properties and to rationalize the origin of the trends. For this, we are systematically exploring the potential energy surfaces for metal dihalides and metal chalcogenides monolayers. 

Graphene and Carbon Materials

Band Gap Tuning of Graphene by Adsorption of Aromatic Molecules

Xiao-Feng Fan, W.T. Zheng, Zexiang Shen, Ai-Qun Liu, Jer-Lai Kuo, Nanoscale. 4, 2157 (2012)  link

The effects of adsorbing simple aromatic molecules on the electronic structure of graphene were systematically examined by first-principles calculations. Adsorptions of different aromatic molecules borazine (B3N3H6), triazine (C3N3H3), and benzene (C6H6) on graphene have been investigated, and we found that molecular adsorptions often lead to band gap opening. While the magnitude of band gap depends on the adsorption site, in the case of C3N3H3, the value of the band gap is found to be up to 62.9 meV under local density approximation—which is known to underestimate the gap. A couple of general trends were noted: (1) heterocyclic molecules are more effective than moncyclic ones and (2) the most stable configuration of a given molecule always leads to the largest band gap. We further analyzed the charge redistribution patterns at different adsorption sites and found that they play an important role in controling the on/off switching of the gap—that is, the energy gap is opened if the charge redistributes to between the C–C bond when the molecule is adsorbing on graphene. These trends suggest that the different ionic ability of two atoms in heterocyclic molecules can be used to control the charge redistribution on graphene and thus to tune the gap using different adsorption conditions.

Figure 4. Area with charge accumulation in several adsorption configurations. (a), (b), and (c) are “cross”, “N-top”, and “C-top” configurations of triazine. Parts (d), (e), and (f) are the “cross”, “AB”, and “bridge” configurations of benzene. All planes are chosen at around z = 0.91.2 Å

Graphene nanoribbon band-gap expansion: Broken-bond-induced edge strain and quantum entrapment

X. Zhang, Jer-Lai Kuo, M. Gu, Ping Bai, and Chang Q. Sun, Nanoscale 2, 2160 (2010) link

An edge-modified tight-binding (TB) approximation has been developed, enabling us to clarify the energetic origin of the width-dependent band gap (EG) expansion of the armchaired and the reconstructed zigzag-edged graphene nanoribbons with and without hydrogen termination. Consistency between the TB and the density-function theory calculations affirmed that: (i) the EG expansion originates from the Hamiltonian perturbation due to the shorter and stronger bonds between undercoordinated atoms, (ii) the combination of the edge-to-width ratio with a local bond strain up to 30% and the associated 152% potential well depression determines the width dependent EG change; and, (iii) hydrogen termination affects insignificantly the band gap width as the H-passivation minimizes the midgap impurity states.

Fig. 1 Crystal structure of an infinitely long GNR shows bare ended (a) AGNR and (b) recZGNR with one edge reconstructed unit cells (gray lines) as well as indication width N, atom positions A–C and the corresponding tij.

Fig. 2 (a) Schematic illustration of the GNR edge bond strain and potential trap. The shorter and stronger edge bonds cause the potential well depression, which enhances the overlap integral according to eqn (2). (b) Correlation between the tij and the bond length d derived from the DFT results33 in comparison to the BOLS prediction.

Water and Hydrogen Bonded Clusters

Structures and Dissociation Channels of Protonated Mixed Clusters around a Small Magic Number: Infrared Spectroscopy of ((CH3)3N)n–H+–H2O (n = 1–3)

Ryunosuke Shishido, Jer-Lai Kuo, and Asuka Fujii,J. Phys. Chem. A, 116, 6740 (2012)  link

The magic number behavior of ((CH3)3N)n–H+–H2O clusters at n = 3 is investigated by applying infrared spectroscopy to the clusters of n = 1–3. Structures of these clusters are determined in conjunction with density functional theory calculations. Dissociation channels upon infrared excitation are also measured, and their correlation with the cluster structures is examined. It is demonstrated that the magic number cluster has a closed-shell structure, in which the water moiety is surrounded by three (CH3)3N molecules. The ion core (protonated site) of the clusters is found to be (CH3)3NH+ for n = 1–3, but coexistence of an isomer of the H3O+ ion core cannot be ruled out for n = 3. Large rearrangement of the cluster structures of n = 2 and 3 before dissociation, which has been suggested in the mass spectrometric studies, is confirmed on the basis of the structure determination by infrared spectroscopy.

Structure and vibrational spectra of H+(HF)n(n = 2 – 9) clusters: An ab initio study

K. B. Sophy and Jer-Lai Kuo, J. Chem. Phys.131, 224307 (2009) link

The morphological development of the hydrogen bond network in the protonated hydrogen fluoride clusters, H+(.HF.)n(.n= 2 – 9)., is investigated in detail by ab initio methods. We find a dominance of the linear morphology, which is energetically well separated from the other minimum energy morphologies of the clusters. The geometry for these clusters shows a pattern due to the cooperativity effect prevalent in the hydrogen bonds, as a result of the difference in electronegativities of hydrogen and fluorine atom in the HF molecule. The variations in the covalent HF and hydrogen bond distances in the clusters are in turn reflected in the vibrational spectra. Distinct HF stretching modes for the linear and ring with tail structures were identified. We have discussed the signature peaks for the two possible ion-core morphologies present in the clusters. The highly corrosive nature of HF makes it difficult to study using experiments. We, thus, believe that our structure and vibrational spectra calculations would be useful in understanding the key features in these systems.

FIG. 3. H+(.HF).n cluster morphologies for n=2–9 found to be local minima from MP2 calculations using 6-311+G.. basis. The ion cores in the structures are marked with red color for shared proton and blue to denote localization of proton on HF molecule.

FIG. 6. Vibrational spectra .unscaled. of the Rt  morphological structures for ring sizes 5, 6, 7, and 8 calculated at the MP2/6-311+G.. level. Symbolic

representation for modes d, e, f, g, h, i, and j arising for the ion core and modes a, b, and c occurring at the AAD site are given below the spectra and color coded to match the colored labeling in the spectra.

Computational Chemistry

Mechanistic Insights into the Substrate-Controlled Stereochemistry 

of Glycals in One-Pot Rhodium-Catalyzed Aziridination and Aziridine Ring Opening

Rujee Lorpitthaya, Zhi-Zhong Xie, Sophy Bhasi Kunnappilly, Jer-Lai Kuo, and Xue-Wei Liu, Chemistry - A European Journal 16, 588 (2010) link

We carried out a principle study on the reaction mechanism of rhodium-catalyzed intramolecular aziridination and aziridine ring opening at a sugar template. A sulfamate estergroup was introduced at different positions of glycal to act as a nitrene source and, moreover, to allow the study of the relative reactivity of the nitrene transfer from different sites of the glycal molecule. The structural optimization of each intermediate along the reaction pathway was extensively done by using BPW91 functional. The crucial step in the reaction is the Rhcatalyzed nitrene transfer to the double bond of the glycal. We found that the reaction could proceed in a stepwise manner, whereby the N atom initially induced a single-bond formation with C1 on the triplet surface or in a single step through intersystem crossing (ISC) of the triplet excited state of the rhodium–nitrene transition state to the singlet ground state of the aziridine complexes. The relative reactivity for the conversion of the nitrene species to the aziridine obtained from the computed potential energy surface (PES) agrees well with the reaction time gained from experimental observation. The aziridine ring opening is a spontaneous process because the energy barrier for the formation of the transition state is very small and disappears in the solution calculations. The regio- and stereoselectivity of the reaction product is controlled by the electronic property of the anomeric carbon as well as the facial preference for the nitrene insertion, and the nucleophilic addition.

Figure 1. Three model compounds for rhodium-catalyzed aziridination.

Figure 2. Computed potential energy surface of rhodium-catalyzed nitrene insertion into the double bond of glycal series 4 at the BPW91/BSI level. Therelative energy values correspond to substrate SMACHTUNGTRENUNG(4 S) (S=restricted singlet state, T=unrestricted triplet state).