A Theoretical Investigation on Photo-Electronic Property of Rac-Catena-Poly [nickel (II)-di-μ-tryptophanato].pdf

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Journal of Optics Applications October 2013, Volume 2, Issue 4, PP.56-62

A Theoretical Investigation on Photo-Electronic

Property of Rac-Catena-Poly [nickel

(II)-di-μ-tryptophanato] Ran Zhang1,3, Ruojing Song2, Yuxi Sun2,3,4,#, Qingli Hao4

1 Institute of material Chemistry, Binzhou University, Binzhou, 256600, P. R. China

2 Key Laboratory of Photoinduced Functional Materials, Mianyang Normal University, Mianyang 621000, P.R. China

3 Key Laboratory of Life-Organic Analysis, Qufu Normal University, Qufu, 273165, P. R. China

4 Key Laboratory of Education Ministry for Soft Chemistry and Functional Materials, Nanjing University of Science and

Technology, Nanjing 210094, P. R. China

# Email: [email protected]

Abstract

In this paper, density functional theory calculation was used to reveal the electron characteristics of rac-catena-poly [nickel

(II)-di-μ-tryptophanato]. In the studied molecule, the Mülliken atomic charges are distributed heterogeneously, and the electrons

in natural bond orbitals are transferred easily among the separated indolyl and Ni-coordinated segments. The electrons are

transferred directionally from the outsider indolyl groups to the medial nickel-coordinated moiety with obvious threshold energies

with absorbed lights of 638.11, 723.77 and 831.48 nm due to the linking bridge composed of the C2-C3-C5 bond, while the

electrons of the medial Ni-coordinated moiety can be redistributed easily in the medial plane with the lowest energy gap 0.3582

eV and the strongest oscillator strength 0.0444. The results indicate the studied compound is a good candidate of potential

photoelectric or bioelectric materials.

Keywords: Nickel-Trytophanato Complex; Photo-Electronic Property; NBO; TD-DFT

1 INTRODUCTION

The molecule with directionally electron-transferred characteristics is the micro-structural foundation of the

bioelectric or photovoltaic material. For example, the photosynthetic organelles of membrane proteins can transport

charges directionally with absorbed ambient photons, and the photovoltaic devices can transfer electrons

directionally to separate charges into different moieties, as result, these materials will present the photosynthetic and

photovoltaic functions. It has been reported that the heterojunction substructure is the key component to perform the

charge separations by the mode of long-range electron transitions in the bioelectric and photovoltaic materials [1-12].

Then the molecular architecture should be the functional foundation toward striking the charge balance and impact

on the charge-transfer interactions to achieve electron separation. So, it is a significant work to find out the key

functional unit in the photo responsive material field.

Biological substances, such as amino acids, peptides, purines, DNA etc with their metal complexes, are generally

accepted as model compounds in biological, medical and chemical fields due to their comprehensive properties [7-19].

Numerous aromatic compounds have been used to construct the photovoltaic devices [20-22]. In particular, the

metal-organic complexes have shown the promising photoelectric functions demonstrated in previous studies [22-26].

Then, it should be a remarkable work to theoretically investigate the electron-transferred structural characteristics of

the metal-organic complexes made by aromatic biological substances and metal ions, which will maybe provide us a

new idea in finding or exploring the photo functional compounds.

These reasons mentioned-above trigger the theoretical exploration of the photo responsive characteristics of the

metal-bioorganic complexes. The tryptophan is the most photosensitive compound among the bioorganic units

mailto:[email protected]

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including amine acids, DNA/RNA bases etc. Since it is very difficult to form metal-organic complexes in the natural

experimental condition for tryptophan, the experimental structures of the complexes formed by tryptophan have been

reported rarely. Examining the corresponding references, the crystal parameters of the nickel-tryptophan complex:

rac-catena-Poly [nickel (II)-di-μ-tryptophanato] ([Ni (L-trp)(D-trp)]n) was reported by Wang in 2009 [27], which

provides the structural foundation in the theoretical calculation. Therefore, the complex was selected in this work,

and its intramolecular electronic properties were revealed by a DFT method. As a result, the promising photovoltaic

characteristics of the studied complex were revealed in this work.

2 COMPUTATIONAL METHOD

Density functional theory (DFT) calculations have successfully carried out to investigate the molecular structures,

vibrational frequencies, NMR, photoelectric properties in chemical, medical and biological fields. The LANL2DZ

basis set has an advantage in the calculations for metals [28]. For meeting the requirements of computing accuracy

and economy, the Becke’s three parameter hybrid functional method combined with the Lee-Yang-Parr correction

functional of DFT (DFT/B3LYP) as well as LANL2DZ basis set was adopted in this work.

As it is well known that the three-dimension geometry taken from X-ray crystallographic data can provide us an

important structural foundation in the theoretical research on complicated molecules. In order to research on the

Ni-trp complex better in this work, the crystallographic data [27] was directly used as the spatial coordinate positions

in the theoretical calculations, and the natural bond orbital (NBO) and time dependent-density functional theory

(TD-DFT) were applied to reveal the photo responsive characteristics relating to the electron transition potentials and

photoelectric properties.

All the calculations were done with Gaussian 03W program software package [29] using the default convergence

criteria on a Dell Core computer.

3 RESULTS AND DISCUSSION

Graphical Abstract

FIGURE 1 THE MOLECULAR DIAGRAM OF THE STUDIED COMPLEX WITH ATOMIC NUMBERING a a The unlabeled atoms in the smallest symmetric unit are obtained by symmetrical operations with symmetry codes: (i) -x,

1-y, 1-z; (ii) –x, -0.5+y, 0.5-z; (iii) x, 1.5-y, 0.5+z.

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In order to state clearly in the context, the smallest molecular unit with the atom numbering scheme for the studied

complex is shown in Figure 1. A central nickel (Ni) atom adopts a six coordinated mode with adjacent four

tryptophans to form a slightly distorted octahedral configuration (Ni1-O1, 2.037(3) Å; Ni1-N1, 2.096(4) Å; Ni1-O2ii,

iii, 2.098(3) Å (ii: –x, -0.5+y, 0.5-z; iii: x, 1.5-y, 0.5+z)) [27]. The coordinated moieties connected by carboxyl groups

form a two-dimensional planar structure, and the neighboring indolyl groups are distributed by a nonparallel mode

on both sides of the planar substructure. The geometry provides us with a good representative model structure for the

investigation on photoelectric properties of metal-organic compounds.

3.1 MÜLliken Atomic Charges

The Mülliken atomic charges of the non-hydrogen atoms for the studied complex are listed in Table 1. Comparison

of these atomic charges shows that the C1 and C5 atoms have relatively positive charges with 0.356437 e and

0.262504 e, respectively, while the N1, C3 and C4 atoms give relatively negative charges with -0.574554 e,

-0.576340 e and -0.509070 e respectively.

TABLE 1 MULLIKEN ATOMIC CHARGES OF THE STUDIED COMPLEX

Atoms Charges Atoms Charges Atoms Charges

Ni1 0.174010 C1 0.356437 C6 0.090554

N1 -0.574554 C2 -0.111396 C7 0.082132

O1 -0.313027 C3 -0.576340 C8 -0.395894

O2 -0.334249 N2 -0.321723 C9 -0.324639

C4 -0.509070 C10 -0.292561

C5 0.262504 C11 -0.468301

FIGURE 2 THE TOTAL CHARGE DENSITY SURFACE IN ELECTROSTATIC POTENTIAL FOR HEXAPLOID

ASYMMETRIC UNIT OF THE STUDIED COMPLEX

On the whole, the indolyl groups and Ni-central coordinated atoms are charged negatively, and the total charge

density surface of the complex is shown in Figure 2 by using ChemOffice 2004 software package of version 8.0 [30].

The medial planar moiety is bridged by the electron-richer carboxyl oxygen atoms, and the photosensitive indoles

with conjugated atoms are separated with each other. Consequently, the electrons may be transferred from the

indolyl moieties to the Ni-carboxyl-bridged plane with the lights absorbing. Yet, the indolyl and Ni-coordinated

moieties are linked by single bonds of C2-C3 and C3-C5, resulting in threshold energy when electrons are

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transported between them. The structure is satisfied with the structural characteristics of the photovoltaic transition

molecular device [31], and it is beneficial to transfer electrons in a long range along with a photon

absorption/emission.

In a word, the charge architecture of the studied complex is possible to transfer electrons in a long range because of

the characteristics of atomic charges.

3.2 Natural Orbital Analysis

According to the natural bond orbital (NBO) basis [32, 33], the orbital interactions result in a loss of occupancy from

the localized NBO of the idealized Lewis structure into an empty non-Lewis orbital. For each donor (i) and acceptor

(j), the stabilization energy E(2) associated with the delocalization i→j is estimated as follows: 2 2

, ,(2)

,

i j i j

i i

j i i j

F FE q q

Here, qi is the donor orbital occupancy, εi and εj are diagonal elements (orbital energies), Δεi,j is energy gap between

donor (i) and acceptor (j) NBO orbitals, and Fi, j is the off diagonal NBO FOCK matrix element.

The NBO data provides the quantitative energies of adjacent orbital interactions with the most accurate ‘natural

Lewis structure’, thus, which can be used to estimate the instantaneous direction for the electron migration of

substructure, furthermore, to reveal the characteristics of intramolecular charge transition with external perturbations

for a studied molecule.

In order to investigate the electron interactions of the studied molecule, the hexaploid structure as shown in figure 1

was computed at DFT/B3LYP-LANL2DZ level and the representative couples of NBO interactions of [Ni(L-trp)

(D-trp)]3 were listed in Table 2.

TABLE 2 SELECTED NATURAL BOND ORBITAL INTERACTIONS OF THE STUDIED COMPLEX

Donor NBO(i) EDi/e Acceptor NBO(j) EDi/e E(2)/kJ/mol Δεi,j/a.u. Fi,j/a.u.

LP (1) N1 1.78512 LP*(5)Ni1 0.68055 101.75 0.18 0.068

LP (1) N1 1.78512 LP*(6)Ni1 0.25860 124.52 0.59 0.119

LP (1) O1 1.95464 LP*(6)Ni1 0.25860 40.08 0.81 0.083

LP (2) O1 1.74840 LP*(5)Ni1 0.68055 109.20 0.17 0.067

LP (2) O1 1.74840 LP*(6)Ni1 0.25860 91.17 0.58 0.100

LP (3) O1 1.60535 LP*(5)Ni1 0.68055 20.00 0.09 0.020

LP (1) O2ii 1.95522 LP*(6)Ni1 0.25860 55.35 0.93 0.105

LP (2) O2ii 1.86166 LP*(6)Ni1 0.25860 31.38 0.54 0.058

LP*(6)Ni1 0.25860 BD*(1) C1ii-O2ii 1.82957 67.20 0.04 0.047

BD (1) C1ii-O2ii 1.82957 BD*(2) C1ii-O1ii 0.23796 162.34 0.84 0.164








LP (2) O2ii 1.86166 BD*(1) C1ii-O1ii 0.11303 69.87 0.66 0.094

LP (2) O2ii 1.86166 BD*(1) C2ii-C1ii 0.08905 68.12 0.66 0.094

BD (2) C10-C11 1.97606 LP (1) C6 1.06081 163.93 0.15 0.089

BD (2) C10-C11 1.97606 BD*(2) C9-C8 0.31995 99.29 0.30 0.076

BD (2) C9-C8 1.74311 BD*(2) C10-C11 0.30641 88.41 0.30 0.072

BD (2) C9-C8 1.74311 BD*(2) C7-N2 0.74936 131.46 0.23 0.088

LP (1) C6 1.06081 BD*(2) C7-N2 0.74936 1183.70 0.07 0.129

LP (1) C6 1.06081 BD*(2) C10-C11 0.30641 286.90 0.14 0.105

LP (1) C6 1.06081 BD*(2) C4-C5 0.31146 321.21 0.12 0.105

BD (2) C7-N2 1.89298 BD*(2) C4-C5 0.31146 74.27 0.38 0.077

BD (2) C7-N2 1.89298 LP (1) C6 1.06081 40.58 0.26 0.061

BD (2) C4-C5 1.85492 LP (1) C6 1.06081 147.90 0.18 0.096

BD represents bond density, BD*represents anti-BD; LP represents lone pair, LP* represents anti-LP; ED presents

electron density; E(2) is interaction energy of adjacent orbitals; Δεi,j is energy gap between donor (i) and acceptor (j) NBO

orbitals; Fi,j is the Fock matrix element between i and j NBO orbitals; Symmetry code: (ii) –x, -0.5+y, 0.5-z.

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As seen from Table 2, the lone pair electrons of oxygen and nitrogen atoms coordinated with nickel ions present

strong charge transfer potentials (226.27 kJ/mol for N1, 260.45 kJ/mol for O1 and 86.73 kJ/mol for O2). The bonds

C1-O1 and C1-O2 exhibit the characteristics of easily transferring electrons to their antibonds, furthermore, the lone

pair electrons of O2 atom bring strong transfer potentials to adjacent antibonds C1-C2 and C1-O1. These results

indicate that the Ni-carboxyl-bridged two-dimensional structure possesses a good charge transfer characteristics.

In the indolyl moiety, the benzene and pyrrole rings exhibit p-electrons conjugated structural characteristics. It is

remarkable that the electrons of the indole present an unequal charge transfer potential, as a result, the charges of the

benzene take away to the pyrrole with a good potential.

Overall, the NBO results show that the electrons-active regions of indolyl and Ni-coordinated moieties of the

complex are also separated from each other due to the connection of single bonds C2-C3 and C3-C5. The results

indicate that the investigated molecule maybe benefit to the formation of a threshold energy when it transfers

electrons, in other words, the electrons may be transported from one conjugated moiety to another when the

molecule absorbs certain photons to overcome the threshold energy.

3.3 Photoelectric Effect

According to frontier molecular orbital (FMO) theory, the electron transitions of compounds are most likely to occur

between two interactive FMOs. In the process of the interaction, electrons move from an occupied molecular orbital

to an unoccupied one along with absorption or emission of photon. The FMOs in the electrons-jumping conditions

are following the rules: (i) they should have the same symmetry as far as possible; (ii) their energies should be close

to each other; (iii) the moving direction of electrons should benefit to weak old bonds and the formation of new

bonds.

According to the previous literatures reporting that the aromatic structures possess photon- and electron-absorption

properties [34-38], these indolyl groups of the investigated complex may be good photosensitive components while the

complex acts as a functional photoelectric material.

In order to reveal the photoelectric properties, the TD-DFT method was adopted to compute [Ni (L-trp)(D-trp)]3 as

the representative structure of the studied complex and the effective electron-transfer details calculated at

DFT/B3LYP-LANL2DZ level are listed in Table 3, including the calculated excitation wavelengths (λ), the vertical

absorption values (Ω), oscillator strength (f) and the mainly contributing orbital transitions.

TABLE 3 SELECTED ELECTRONIC ABSORPTION VALUES FOR THE STUDIED COMPLEX

λ /nm Ω /eV Oscillator strengths (f) Electronic transitions

3461.01 0.3582 0.0444 HOMO→LUMO (100%)

831.48 1.4911 0.0019 HOMO-1→LUMO+1 (75.9%)

723.77 1.7130 0.0023 HOMO-6→LUMO (74.0%)

638.11 1.9430 0.0121 HOMO-9→LUMO (57.4%)

A long-range electron transition will produce a p-n junction so that it is the most concern to the researcher of

photovoltaic systems. In order to study the electronic distributions of active orbitals, these molecular orbitals listed in

Table 3 are shown in Figure 3 by GaussView 3.0 software [39]. As seen from the Figure 3 and Table 3, all the

transitions comply with the electron-transfer principle, and the strongest electron transition is shown by the highly

symmetric HOMO and LUMO orbitals with oscillator strength 0.0444, while other transitions present lower

oscillator strengths. By comparison of these excitable FMOs, it can be found that the electron distributions of the

orbitals are different from each other. As expected, the LUMO+1 and LUMO as acceptor orbitals are essentially

localized at the Ni-coordinated medial moiety, and HOMO-1, HOMO-6 and HOMO-9 as donor orbitals are

principally localized in the indolyl groups. Thus, the complex can theoretically absorb the lights of 638.11 nm,

723.77 nm and 831.48 nm, accompanying with the transporting electrons from outside indoles to medial

Ni-coordinated moiety with respective weaker oscillator strengths 0.0019, 0.0023 and 0.0121 indicating obvious

threshold energies, while the electrons of the medial Ni-coordinated moiety can be distributed easily in the medial

plane as shown by the HOMO and LUMO with the lowest energy gap 0.3582 eV and the strongest oscillator strength

0.0444. The results indicate that the complex has the promising photovoltaic characteristics with the

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electron-migration pattern of the electron transition from outside indoles to the medial Ni-coordinated moiety and the

electron redistribution in the medial plane.

FIGURE 3 SURFACES OF FMOs FOR THE STUDIED COMPLEX

4 CONCLUSIONS

The rac-catena-Poly [nickel (II)-di-μ-tryptophanato] was objectively selected as a photovoltaic model of

metal-organic compounds, and its photoelectric properties were revealed by the theoretical data calculated at

DFT/B3LYP-LANL2DZ level. The mülliken atomic charge distributions are heterogeneous, and the electrons in

natural bond orbitals are transferred easily among the separated indolyl and Ni-coordinated segments due to the

connection of single σ-type bonds C2-C3 and C3-C5. As expected, the investigated complex shows a promising

photovoltaic property with electron transitions from outside indoles to the medial moiety with absorbing lights of

638.11, 723.77 and 831.48 nm.

The reported results are of assistance for theoretical evidences in the quest of new functionally photovoltaic and

bioelectric materials, and promote the application of metal-organic compounds in the new energy and bioelectronic

fields.

ACKNOWLEDGEMENTS

This work was supported by Natural Science Foundations of China (Nos. 21073092 & 21103092), Sichuan

Education Department Fund (No. 12ZA080), Scientific Research Foundation for Excellent Plan of Binzhou

University (BZXYQNLG200704) and Mianyang Normal University for Excellent Plan Fund (No. QD2012A06).

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A Theoretical Investigation on Photo-Electronic Property of Rac-Catena-Poly [nickel (II)-di-μ-tryptophanato].pdf