Perspective: On the relevance of slower-than-femtosecond time scales in chemicalstructural-dynamics studiesPhilip Coppens Citation: Structural Dynamics 2, 020901 (2015); doi: 10.1063/1.4913362 View online: http://dx.doi.org/10.1063/1.4913362 View Table of Contents: http://scitation.aip.org/content/aca/journal/sdy/2/2?ver=pdfcov Published by the American Crystallographic Association, Inc. Articles you may be interested in Femtosecond streaking of electron diffraction patterns to study structural dynamics in crystalline matter Appl. Phys. Lett. 102, 121106 (2013); 10.1063/1.4798518 Interplay between magnetism and chemical structure at spinel-spinel interfaces J. Appl. Phys. 111, 093903 (2012); 10.1063/1.4707890 Stability of rare gas structure H clathrate hydrates J. Chem. Phys. 125, 104501 (2006); 10.1063/1.2238864 Ultrafast excited-state dynamics in photochromic N-salicylideneaniline studied by femtosecond time-resolvedREMPI spectroscopy J. Chem. Phys. 121, 9436 (2004); 10.1063/1.1801991 X-ray and Raman scattering study of C 60 -biphenyl single crystals AIP Conf. Proc. 591, 153 (2001); 10.1063/1.1426842

Perspective: On the relevance of slower-than-femtosecondtime scales in chemical structural-dynamics studies

Philip CoppensChemistry Department, University at Buffalo, SUNY, Buffalo, New York 14260-3000, USA

(Received 23 January 2015; accepted 9 February 2015; published online 24 February 2015)

A number of examples illustrate structural-dynamics studies of picosecond and

slower photo-induced processes. They include molecular rearrangements and exci-

tations. The information that can be obtained from such studies is discussed. The

results are complementary to the information obtained from femtosecond studies.

The point is made that all pertinent time scales should be covered to obtain compre-

hensive insight in dynamic processes of chemical and biological importance.VC 2015 Author(s). All article content, except where otherwise noted, is licensedunder a Creative Commons Attribution 3.0 Unported License.

[http://dx.doi.org/10.1063/1.4913362]

I. INTRODUCTION

Time-resolved diffraction studies have a long history, but the definition of the concept

time-resolution is broadly defined, and is used to describe a range of events from plate tectonics

to electronic excitations and beyond. In Biology, Chemistry, and Material Science, the range is

continuously expanding towards faster events and now includes ultrafast processes taking place

in femtoseconds, driven by revolutionary technological developments. Spectacular new experi-

mental information is becoming available on such timescales. New insight is gained in the ini-

tiating stages of dynamic processes like chemical reactions. However, novel dynamic informa-

tion accessible in slower time domains is often complementary and frequently relevant in its

own right. Some such information is summarized in Scheme 1. Whereas, the ultrafast

femtosecond-timescale experiments give information on a timescale of instantaneous atomic

motions, the slower ones typically provide information on the statistically averaged response of

an assembly of molecules, related to the structural changes and kinetics of the system studied.

The study of photo-induced processes in crystals is generally referred to as photocrystallog-

raphy. The well-defined structural environment of the photo-products in periodic crystals often

has to be taken into account to reproduce the observations theoretically. The impact of the ma-

trix surrounding the active species is by itself of more than fundamental interest as materials

used in practical devices are typically solids.

We present a number of selected examples highlighting the application of structural dy-

namics studies of processes that proceed on slower timescales than femtoseconds, on which cur-

rently much attention is focused.

II. DIFFERENT TIME-DOMAINS

A. Processes taking hours

Chemical reactions in crystals tend proceed relatively slowly, but can be studied by diffrac-

tion methods at atomic resolution, in particular, if the reactions proceed in a topotactic way,

which implies that the integrity of the crystal lattice is preserved in a single-crystal-to-single-

crystal reaction. Time-dependent studies on the timescale of hours give information on the pro-

gress of a reaction within the periodic assembly of molecules and on the activation energies of

the reaction if temperature dependent studies are included, rather than on the instantaneous

mechanism of the reaction, which requires sub-picosecond studies. An example is the study of

2329-7778/2015/2(2)/020901/8 VC Author(s) 20152, 020901-1

STRUCTURAL DYNAMICS 2, 020901 (2015)

the small olefin trans-tiglic acid (TA) (Scheme 2), which undergoes trans-cis photoisomerization

around the C¼C bond (Fig. 1). In a study of the Zn-(tiglic acid)2 complex in a CECR matrix

(Scheme 2, Fig. 3), the measurements were performed at four different temperatures in the

90–190 K range. The crystal contains two tiglic acid molecules in the asymmetric unit, both

complexed to the same Zn atom, as shown in Figure 2. But the two molecules are located in

cavities of very different sizes, indicated by the different color ellipses in Fig. 3. This implies

SCHEME 1. Time scales of dynamic processes in molecular sciences.

SCHEME 2. Structures of (a) tiglic acid, (b) C-ethyl calixarene (CECR).

FIG. 1. The trans-cis reaction of tiglic acid.

020901-2 Philip Coppens Struct. Dyn. 2, 020901 (2015)

that TA molecule, encircled by the blue ellipse in Fig. 2, is more constrained than the second

one within the red ellipse in the figure. Both the reaction rates and the composition of the pho-

tostationary states are strikingly different, as shown in detail in the reference (Zheng et al.,2008). Subsequent Arrhenius and Eyring kinetic plots lead to energies and enthalpies of both

the forward and reverse crystal reactions amounting to several kJ mol�1. The results give quan-

titative evidence for the constraining effect of the crystal environments on the reaction, which

is as expected more severe for the smaller cavity.

The photoinduced reactions of cinnamic acid and derivatives remain some of the most

studied solid state [2þ 2] photodimerizations since the pioneering studies of Schmidt and

FIG. 3. Data point is based on refined occupation parameters. Converted fraction of a-cinnamic acid as a function of irradi-

ation time. The curved line is a fit with n¼ 1.43 and k¼ 6.5 � 10�5 -s�1. Reprinted with permission from Benedict, J. B.

and Coppens, P., J. Phys. Chem. 113, 3116–3120 (2009). Copyright 2009 American Chemical Society.

FIG. 2. 3D-supramolecular architecture viewed along the b-axis direction (Zn atom is displayed as a sphere). Large and

small cavities marked by red and blue ellipses, respectively.

020901-3 Philip Coppens Struct. Dyn. 2, 020901 (2015)

co-workers in the sixties established the topochemical principles governing such reactions

(Cohen et al., 1964; Schmidt, 1964; 1971). The kinetics of the dimerization reaction in a series

of compounds has been analyzed by the JMAK kinetics of Johnson, Mehl, Avrami, and

Kolmogorov (Kolmogorov, 1937; Avrami, 1939; and Johnson and Mehl, 1939). Crystals of a-

cinnamic acid were studied by two-photon excitation (Benedict and Coppens, 2009), which

increases the likelihood of single-crystal-to-single-crystal transformations (Naumov et al., 2002;

Harada et al., 2008). The fraction converted vs. time curve is S-shaped (Fig. 3). A fit of the

curve against the equation y ¼ e�ktn , where y is the conversion percentage and n is related to

the dimensionality of the seed growth of the nucleus, with a value of n¼ 1 corresponding to an

equal-growth probability in all directions. For the a-cinnamic acid polymorph n was found to

be 1.43 (8) (Fig. 3), suggesting a hybrid mechanism combining homogeneous nucleation with

one-dimensional growth of the nuclei. The results agree within the experimental uncertainties

with an earlier solid state NMR study which led to an n value of 1.66 (Bertmer et al., 2006). In

a subsequent study of the molecule 1,4-dimethylpyridone surrounded in the lattice by a cavity

formed by inactive hosts at 230 K and 280 K, a similar hybrid model of the dimerization was

found with n¼ 1.6 (1) and 1.5 (1) at the two temperatures, respectively. An activation energy

of 32.5 kJ/mol was calculated from the kinetic plot. A very different Avrami exponent of 0.55

was found for the [4þ 4] photodimerization of 9-anthracene carboxylic acid (Taylor et al.,1998). It would imply a negative dimensionality, a result interpreted as a negative autocatalytic

step, or auto inhibition, during the photoreaction (Mor�e et al., 2010). Further studies on addi-

tional systems are needed before a comprehensive theory on the progress of this type of reac-

tions in crystals can be formulated.

B. Timescales of milliseconds

Many photo-induced processes in the solid state involve the intramolecular rearrangement

of groups of atoms or transfer of atoms to different parts of a molecule. Linkage isomerizations

were already reviewed in 1968 (Burmeister, 1968). The kinetics of the rearrangements is typi-

cally temperature-dependent, with many of the isomers being unstable at room temperature.

However, at reduced temperatures intermediates and final products can be identified. Species

discovered on light-exposure of sodium nitroprusside Na2[Fe(CN)5(NO)]�2H2O were originally

described as electronically excited states with unusually long lifetimes at 100 K (Hauser et al.,1977b; 1977a). However, crystallographic studies in the mid-nineties showed that they are in

fact metastable linkage isomers in which the nitrogen-bound NO group is either inverted or

sideways bound, as illustrated in Fig. 4 (Carducci et al., 1997). Many chemically related com-

plexes undergo similar isomerizations (Coppens et al., 2002; Bitterwolf, 2006) and extensive

photocrystallographic work is continuing. The rearrangements of many of such compounds are

accompanied by color, refractive index, and magnetic changes and have potential for use in op-

tical switching and memory devices (G€utlich et al., 2001; Fally et al., 2004; and Schaniel

et al., 2007).

FIG. 4. The nitroprusside ion (left) and its photo-induced linkage isomers.

020901-4 Philip Coppens Struct. Dyn. 2, 020901 (2015)

Reduction of the temperature slows down the decay processes and allows identification of

possible intermediates and, by measurement of the decay at different temperatures, determina-

tion of the kinetics and identification of possible intermediates. This approach has been pursued

by Hatcher, Raithby, and co-workers. They report photo-activated reorientation of one of the

nitro groups in [Ni(Et4dien)(g2-O,ON)(g1-NO2)] (Et4dien¼N,N,N0,N0 tetraethyldiethylenetri-

amine). The group rearranges from N-bound g1-NO2 to O-bound g1-ONO (nitrito) (Figure 5),

on exposure to 500 nm light (Hatcher et al., 2014; Hatcher et al., 2011). Variable temperature

studies in the 150–165 K range show the activation energy of decay to be 48.6 kJ/mol. A second

“pseudo steady-state” experiment with continuous light exposure give evidence for a transient

intermediate species existing in the 145–165 K region in which the g1-ONO nitrito group is dif-

ferently oriented. The laser pump/X-ray pulse technique with variable pump-probe delay times,

discussed in Sec. II C, is well suited for the identification of intermediates, as illustrated by the

detailed studies on the photo-induced cycle of photo-active-yellow protein (PYP) (Tripathi

et al., 2012; Ihee et al., 2005; and Anderson et al., 2004).

C. Timescales of microseconds and nanoseconds: The pump-probe technique

Triplet and singlet photo-induced excited states of molecular species, with typical lifetimes

of microsecond and nanoseconds, respectively, tend to be highly reactive and precursors of pho-

tochemical reactions. Such lifetimes are well matched to the time-resolution of synchrotron

sources with their �50–100 ps time limit imposed by the pulse lengths of the sources. Time-

slicing methods can produce shorter pulses (Schoenlein, 2000), but imply a considerable loss in

intensity, which is prohibitive for many experiments.

Which structural and electronic features of the excited states are responsible for the high

reactivity of the photo-excited states? Once their structure has been determined, theoretical cal-

culations can provide insight in the second part of this question.

The first atomic-resolution studies reported involved binuclear metalorganic complexes

with the metal atom having d7, d8, or d10 configurations. A contraction of the molecule on exci-

tation, resulting from a promotion of an electron from an anti-bonding to a weakly bonding or-

bital, was observed when the first results on the 50 ls lifetime 16 K excited state structure of

[Pt2(P2O5H2)4]4� became available (Novozhilova et al., 2003; Kim et al., 2002). Contractions

FIG. 5. Diagram of [Ni(Et4dien)(g2-O,ON)(g1-NO2)], showing. O-bound g1-ONO (nitrito) and the (g2-O,ON) nitro group

after irradiation with 500 nm light in which the N-bound NO2 group has been reoriented to O-bound.

020901-5 Philip Coppens Struct. Dyn. 2, 020901 (2015)

of binuclear complexes on excitation have since been observed in several systems (Coppens

et al., 2004; Zheng et al., 2005; and Makal et al., 2011). Structural modifications have been

determined for spin-crossover systems, which can be switched between low- and high-spin

states by light irradiation, temperature variation, and other external perturbations, with parallel

changes occurring in magnetic and optical properties (Cailleau et al., 2010).

Many crystals contain more than one molecule in the asymmetric unit. Such chemically

equivalent, but crystallographically independent molecules can show different distortions on ex-

citation and differences in wavelength and lifetime of their luminescence (Makal et al., 2012;

Coppens et al., 2013). Comparison of results of isolated-molecule calculations with calculations

in which the lattice is taken into account confirms such differences. Large differences are often

observed, as in the recent study of a Ag-Cu coinage metal complex, in which theoretical con-

traction of �0.534 and �0.932 A, were reduced to �0.345 and 0.438 A, respectively, when the

environment was taken into account in the calculation, in much better agreement with the ex-

perimental results (Jarzembska et al., 2014). The photodifference maps and the structural

changes on excitation are illustrated in Fig. 6.

Other studies involve intramolecular electron transfer (MLCT, metal-to-ligand charge trans-

fer), in a number of highly luminescent Cu(I) dimethyl-phenanthroline photosensitizer com-

plexes (Vorontsov et al., 2009; Makal et al., 2012). Such complexes are typical for use as

light-emitting diodes (Armaroli et al., 2006; Yersin et al., 2011). Bi-molecular excimer forma-

tion has been observed in crystals of [[3 5–(CF3)2pyrazolate]Cu]3 through photoinduced dimeri-

zation of a pair of molecules with a molecular stack (Vorontsov et al., 2005).

FIG. 6. (a) Photodifference map ofAg2Cu2L4. Solid and transparent surfaces at 0.55 and 0.35 eA�3, respectively. (b) The

observed change from Z- to rhomb-shape of the central cluster due to shortening of the Ag-Cu and Ag-Ag distances on ex-

citation by 0.4–0.5 A. (c) Photodeformation map based on the refined model; blue: positive, red: negative. Reprinted with

permission from Jarzembska et al., Inorg. Chem. 53, 10594–10601 (2014). Copyright 2014 American Chemical Society.

020901-6 Philip Coppens Struct. Dyn. 2, 020901 (2015)

A 100 ps time resolved study at the Advanced Ring at the Photon Factory at KEK on the

photo-induced the neutral (N) to ionic (I) phase transition in tetrathiafulvalene (TTF)-chloranil

was reported by Collet and co-workers (Guerin et al., 2004; Collet et al., 2003). The transition

was first discovered as a thermal process occurring at Tc¼ 81 K (Torrance et al., 1981). It

involves dimer formation along heterogeneous stacks with ferroelectric ordering in the I stacks,

consisting of positive donor (D) TTF molecules and negative acceptor (A) chloranil species.

The transition involves a space group change in which a center of symmetry disappears in the

low-temperature-stable I phase which can be photochemically converted to N at 70 K, while the

reverse process can be triggered above Tc. Time-resolved analysis of changes in the diffuse

scattering pattern at the 50 ps resolution available at the Advanced Ring, allowed identification

of I precursor strings of at least eight (Dþ A�) pairs being generated in the N columns prior to

completion of the phase transition (Guerin et al., 2010).

Overall, the microsecond-nanosecond domain allows investigation of a large number of

excitations with the concomitant change in properties. The field is largely unexplored.

III. CONCLUDING REMARKS

We conclude that many significant scientific issues remain to be addressed on the slower-

than-femtosecond timescales. Structural information can be obtained at atomic resolution and is

often complementary to what can be achieved at femtosecond time scales, at which the impor-

tant initial stages of chemical processes can be revealed. The pronounced shape-changes of

photactive yellow protein on exposure to blue light, for example, are triggered by a trans-cis

isomerization of the p-coumaric acid chromophore, the initial stages of which have not yet

been explored, but the subsequent dynamic isomerization processes are to be studied at slower

time scales (Schmidt et al., 2013; Tenboer et al., 2014), as was done for the related isomeriza-

tion of tiglic acid described above. Many commercial applications involve the millisecond to

nanosecond time domains. They include luminescence, optical switching, biological processes,

and catalysis. Structural dynamics studies remain essential for their elucidation.

ACKNOWLEDGMENTS

Support for this work by the National Science Foundation (No. CHE1213223) is gratefully

acknowledged.

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