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Page 1 of 22 The Journal of Physical Chemistry

Hz1

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FT

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The Journal of Physical Chemistry 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Chemical structures of dl-norleucine, and dl-methionine. In dl-methionine the second to last CH2 group is replaced with sulfur 29x10mm (300 x 300 DPI)

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The Journal of Physical Chemistry

THz absorption spectra of dl-norleucine, measured at room temperature (red), 150K (green), and 100K (blue). The black line represents the calculated results convoluted with a 0.1 THz line width and frequency-scaled by 0.93. The main feature of the measured spectra is reproduced, and the strength of the lower energy resonance was overestimated in the calculation. Inset, structure of dl-norleucine. 54x37mm (300 x 300 DPI)



THz absorption spectrum of dl-methionine, measured at room temperature (red), 150K (green), and 100K (blue). The black line represents the DFT calculation results, convoluted with a 0.1 THz line width and scaled by 0.95. The main feature is reproduced in the measurements, the strength of the weaker resonances is overestimated in the calculation. Inset, structure of dl-methionine. 54x37mm (300 x 300 DPI)


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Mode characteristics of the five strongest modes in a) dl-norleucine compared to b) dl-methionine. The contribution of intra-molecular movement is plotted in black, while the inter molecular movement is separated in translation of a molecule with respect to the center of the unit cell (red) and rotation/libration of this molecule (blue). The percentages are the average over all 8 molecules in the unit cell. To quantify the relative important of each mode, the IR-intensity I0 is noted in the graph, and the modes discussed in detail are highlighted in green and cyan. 63x25mm (300 x 300 DPI)



Eigenvectors at the resonance frequencies. The diameter of the green spheres is proportional to the mass-weighted displacement of that atom for a given eigenvector. a) dl-norleucine at 1.87 THz b) dl-methionine at 1.94 THz. The ammonium, carboxylate group, and the last CH3 group have the greatest contribution to the vibrational mode. c) dl-methionine at 2.49 THz. A corresponding mode does not exist in dl-norleucine. There is larger displacement of the atoms in the side chain for this resonance as seen by the significantly larger diameters compared to b). 53x18mm (300 x 300 DPI)


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Terahertz Spectroscopy and Density Functional Theory Calculations of dl-Norleucine and dl-Methionine †

Jens Neu,

†Yale ‡Yale ¶Current

†,¶

Heinrich Nikonow,

and Charles A. Schmuttenmaer

∗,†,‡

University, Department of Chemistry, New Haven, CT, USA

University, Energy Science Institute (ESI), New Haven, CT, USA

address: University of Heidelberg, Department of Chemistry, Heidelberg, Germany

E-mail: [email protected]

1



Abstract We present Terahertz (THz) measurements and density functional theory (DFT) calculations of two amino acid crystals: dl-norleucine and dl-methionine. Their molecular structures are very similar, and therefore also their crystal structures. We report the absorption spectra for both amino acids which have a strong resonance at 1.87 THz in dl-norleucine, and 1.94 THz in dl-methionine. In addition, we nd a higher frequency resonance at 2.49 THz in dl-methionine which has no corresponding mode in dl-norleucine. The experimental data are supported by DFT calculations which show that the origin of the two strongest vibrational modes in dl-norleucine and dlmethionine are based on the same underlying vibrational motions, while the 2.49 THz resonance in dl-methionine is due to the motion of the sulfur atom, which is not present in dl-norleucine.

Introduction The human metabolic system requires nine essential amino acids. Additionally, 12 nonessential amino acids are found in naturally occurring organisms, and an even larger number of amino acids have been synthesized in the lab 1 . These synthetic, non-natural amino acids are not found in any wild-type organism. However, in recent years, mutants have been grown in which synthetic amino acids are incorporated 2 . It is interesting to consider two very similar amino acids: the essential methionine, and the non-natural norleucine. The dierence between these amino acids is found only in the second to last moeity in the Rgroup sidechain, where it is a methylene group in norleucine and sulfur in methionine (See Figure 1). Replacing naturally occurring methionine with norleucine has been demonstrated for proteins 3,4 , enzymes 5 , and bacteria 6 . In some of these cases, the replacement can be achieved by simply growing the bacteria in a norleucine-rich and methionine-depleted environment 7 . These impressive experiments demonstrate that the binding mechanism between the bacterial backbone and the two amino acids is independent of the sulfur atom. However, 2


Page 8 of 22

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Figure 1: Chemical structures of dl-norleucine, and second to last CH2 group is replaced with sulfur.

dl-methionine.

In

dl-methionine

the

the resulting functionality of the bacteria or enzyme changes drastically when methionine is replaced with norleucine 5 , making this pair an ideal tool for bioengineering. It is also worth noting that methionine does not form sulfur-sulfur linkages as is the case with cystein, the other sulfur-containing proteinogenic amino acid. Therefore, the functionality changes are not due to changes in chemical bonding. The two pure crystals exhibit similar physical and chemical properties. Both amino acids in a racemic mixture form a crystalline structure consisting of eight molecules per unit cell. The two crystals have the same space group (C2/c) and the three lattice constants are within 2% of each other 8,9 , see Table 1 . As a result, crystallographic investigations demand high quality crystalline samples. This similarity also applies for IR spectroscopy, with both amino acids exhibiting similar absorption features between 1600 cm−1 and 600 cm−1 10,11 . Terahertz (THz) spectroscopy 1214 covers the frequency range between 10-100 cm−1 (0.3 to 3.0 THz) 15 and has been demonstrated as a powerful technique to identify chemical compounds 1618 , dierent amino acids 1922 , and even dierent polymorphs of the same amino acids 23,24 . Combined with density functional theory (DFT) calculations, THz spectroscopy can be used to understand the vibrational motions in ordered crystalline structures. We present THz spectroscopic measurements of two crystalline amino acids, dl-methionine and

dl-norleucine.

The low frequency range between 0.3 and 3 THz is particularly sensitive to

the geometry of the unit cell and the vibrational modes are delocalized among many atoms in the unit cell. As a result, replacing a CH2 group in the unit cell with a sulfur aects the vibrational modes in this low energy range. We present experimental spectra which show 3



a frequency shift between

dl-methionine and dl-norleucine.

THz mode which is present only in

Page 10 of 22

We also present and discuss a

dl-methionine, allowing for its easy identication.

The

DFT calculations are used to explain the origin of the dierent modes, and to demonstrate the inuence of the sulfur atom compared to CH2 .

Experimental Setup and Sample Preparation The apparatus used in this experiment is standard THz time-domain spectrometer (THzTDS). The pulse was generated with an interdigitaded photoconductive antenna 25 which was biased with a 5 kHz, 10 V square-wave function and photoexcited by a 50 fs pulse with 100 mW optical power. The THz beam was routed via four o-axis paraboloidal mirrors through the sample onto the detector. The detector was a photoconductive dipole antenna with a 5 µm gap. The usable bandwidth spanned 0.5 THz to about 3 THz. The sample was mounted in a temperature controlled nitrogen cryostat, as described in more detail in previous publications 23,26 . The structure and vibrational modes were calculated using the

Figure 2: THz absorption spectra of dl-norleucine, measured at room temperature (red), 150 K (green), and 100 K (blue). The black line represents the calculated results convoluted with a 0.1 THz line width and frequency-scaled by 0.93. The main feature of the measured spectra is reproduced, and the strength of the lower energy resonance was overestimated in the calculation. Inset, structure of dl-norleucine. SIESTA v3.2r462 package, assuming periodic boundary conditions. We employed the vdW4


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DF-cx pseudo-potentials 27 and triple-zeta, doubly polarized (TZDP) basis set as described in previous publications 23,28 .

dl-methionine

was purchased from Fluka (99% pure) and

dl-norleucine

from Alfa

Aesar (98%). The amino acids were ball-milled to ensure grain sizes of less than 5 µm. These grains were mixed with Teon in a mass ratio of approximately 96 to 4 (Teon to amino acid). The small grains ensure a homogeneous mixture and random orientation. This mixture was pressed into a pellet using a pressure of 11 kbar. The resulting sample had a diameter of 13 mm and was 2.5 mm thick, which allows the THz-data to be truncated in the time domain, eliminating reections and resulting etalon eects. THz transmission of the sample was measured and referenced to an air measurement. From these two measurements we calculated the complex refractive index of the mixed sample. Using eective medium theory, we calculated the real refractive index and the absorption coecient of the amino acid. A more detailed explanation of the data processing can be found in 23 .

Experimental and Computational Results Temperature-dependent THz absorption spectra for

dl-norleucine

are plotted in Figure 2.

At room temperature (red line) the spectrum shows a broad absorption around 1.87 THz and multiple unresolved absorptions around 1.4 THz and 1.6 THz. These absorption features are broadened due to the high temperature of the crystal (290 K, or 25 meV) compared to the THz photon energy (2-8 meV). Hence, a clear identication of characteristic absorptions at room temperature is only feasible if the absorption is particularly strong. A second measurement was performed with the sample cooled to 150 K (green line). The measured spectrum displays sharper features compared to the room temperature spectrum. The strong resonance at 1.87 THz is narrower with a full width at half maximum (FWHM) of 0.34 THz. Furthermore, a lower frequency resonance can now be clearly identied at

5



Page 12 of 22

1.4 THz. This change in the spectrum is due to the narrowing of absorption lines with decreasing temperature 28 . The third measurement at 100 K (blue line) clearly shows the same features as that at 150 K. However, the characteristic absorptions are more pronounced and allow a clear identication of the resonance frequencies at 1.87 THz and 1.44 THz. Table 1:

Starting geometry of the optimization from the CCSD database and

DFT optimized structure, calculated using SIESTA.

dl-Nle

a [Å] b [Å] c [Å] α[◦ ] β[◦ ] γ[◦ ] Spacegroup Z Ref.

dl-Met

dl-Nle

DLNLUA02 DLMETA08 SIESTA 31.67 9.88 30.88 4.72 4.69 4.79 9.85 32.60 9.85 90.0 90.0 90.0 91.4 106.3 90.2 90.0 90.0 90.0 C2/c C2/c C2/c 8 8 8 8 9 this work

dl-Met

SIESTA 9.88 4.76 32.60 90.0 106.0 90.0 C2/c 8 this work

DFT calculations were performed in order to help interpret the experimental results. The atomic coordinates for these calculations were obtained from single crystal XRD data measured at 120 K 8 , as archived in the Cambridge Crystal Structure Database (CCSD, Database Identier DLNLUA02). The unit cell was then optimized using SIESTA-DFT calculations at 0 K, and the vibrational modes were then calculated. The calculated spectra were normalized to the strongest peak, and are plotted as a black line in Figure 2 using a Lorentzian shape with a line width of 0.1 THz (full-width at half-maximum). There is excellent agreement between the primary experimental peak and that of the calculation. The calculation overestimates the intensity of the smaller feature near 1.4 THz. This is because the calculations correspond to 0 K, whereas the experimental spectra were obtained at 100 K (∼ = 8.6 meV ∼ = 2 THz) or higher. Therefore, a lower energy resonance will have a signicant contribution from hot band transitions, resulting in broadening, which causes the experimental resonance to become less pronounced. 6


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The second amino acid considered is in the fth CH2 in structure of

dl-norleucine

dl-methionine

dl-methionine.

These two amino acids dier only

which is replaced by sulfur in

dl-methionine.

The crystal

can be found in CCSD as DLMETA08 9 . The crystallographic

and DFT lattice parameters for the two amino acids are compared in Table 1. It is important to note that the lattice axis labels dier. The a-axis in

c-axis in

dl-methionine.

dl-norleucine

corresponds to the

Both crystals have the same space group and comparable lattice

parameters.

Figure 3: THz absorption spectrum of dl-methionine, measured at room temperature (red), 150 K (green), and 100 K (blue). The black line represents the DFT calculation results, convoluted with a 0.1 THz line width and scaled by 0.95. The main feature is reproduced in the measurements, the strength of the weaker resonances is overestimated in the calculation.Inset, structure of dl-methionine. The measured THz spectrum is shown in Figure 3. At room temperature three broad absorptions can be seen, although a clear identication is challenging due to broadening. The main absorption is located at 1.9 THz, slightly blue-shifted compared to

dl-norleucine.

This becomes more apparent when the sample is cooled down to 100 K. At this temperature, three features are identied. The strongest absorption is located at 1.94 THz and has a line width of 0.2 THz, and two weaker resonances are detected at 1.5 THz and 2.49 THz. Comparing the measured spectra provides two clear ways to identify the dierent amino acids. The rst is the frequency shift of the two lower frequency modes. The lowest detectable resonance for

dl-norleucine is located at 1.4 THz and the corresponding resonance 7



in

dl-methionine

Page 14 of 22

is located at 1.5 THz. Furthermore, the strongest resonance for

norleucine is measured at 1.87 THz, while the strongest absorption in

dl-

dl-methionine is lo-

cated at 1.94 THz. The spectral dierence of 80 GHz can be used to identify the two amino acids. In addition,

dl-methionine shows a resonance at 2.49 THz, which is not detectable in

dl-norleucine. The DFT calculations are in agreement with the experimental results. As noted previously, the DFT optimization begins with atomic coordinates determined from experimental XRD measurements 9 . The spectrum was calculated based on this optimization and is plotted as black line in Figure 3. The three experimental absorption features are reproduced by the calculation. As discussed for

dl-norleucine, the low energy resonance was overestimated

by the DFT calculation.

DFT Calculations of Mode Character

Figure 4: Mode characteristics of the ve strongest modes in a) dl-norleucine compared to b) dl-methionine. The contribution of intra-molecular movement is plotted in black, while the inter molecular movement is separated in translation of a molecule with respect to the center of the unit cell (red) and rotation/libration of this molecule (blue). The percentages are the average over all 8 molecules in the unit cell. To quantify the relative important of each mode, the IR-intensity I0 is noted in the graph, and the modes discussed in detail are highlighted in green and cyan. 8


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The optimized crystal structure was used to calculate the force matrix. The eigenvalues of this matrix correspond to the resonance frequencies of the unit cell 26 . For each of these frequencies, the IR intensity was calculated using the Berry phase approach to calculate the macroscopic polarization 29 and the Born eective charge tensor 30 . Based on the eigenvectors of each atom in the unit cell, we calculated the mode characteristic of the molecules in the unit cell 28 , plotted in Figure 4. We distinguish between intramolecular resonances and intermolecular rotational/librational and translational motions. This analysis shows that the THz resonances in dl-methionine and dl-norleucinecan be described as superposition of intramolecular motions and rotation/libration of the molecules as a whole in the unit cell, and that the translational contribution is negligible. It is particular interesting that in tion, while in

dl-norleucine

dl-methionine

the intermolecular rotation is the strongest contribu-

the intramolecular modes are as strong as the intermolecular

contribution. A more detailed understanding of the resonant modes is achieved by eval-

Figure 5: Eigenvectors at the resonance frequencies. The diameter of the green spheres is proportional to the mass-weighted displacement of that atom for a given eigenvector. a) dl-norleucine at 1.87 THz b) dl-methionine at 1.94 THz. The ammonium, carboxylate group, and the last CH3 group have the greatest contribution to the vibrational mode. c) dl-methionine at 2.49 THz. A corresponding mode does not exist in dl-norleucine. There is larger displacement of the atoms in the side chain for this resonance as seen by the signicantly larger diameters compared to b). uating the individual mass-weighted eigenvectors for each atom. These vectors visualize the contribution of each atom to the resonant modes. The strongest resonant mode in 9



dl-norleucine

(1.87 THz) and

dl-methionine

Page 16 of 22

(1.94 THz), as well as the unique mode in

dl-methionine (2.49 THz) are evaluated in detail here.

For clarity, only one molecule in the

eight molecule unit cell is shown in Figure 5 and the hydrogen atoms are not displayed. The magnitude of an atomic displacement for a particular mode (eigenvector) is represented as the diameter of the sphere around the corresponding atom, plotted in green. This is more intuitive in some respects than the actual eigenvectors which can point into or out of the plane of the image, making it challenging to read-out their length in a 2D visualization. The larger this sphere, the more movement the atom undergoes during the vibration. Figure 5 a) visualizes the main resonance mode of

dl-norleucine, and Figure 5 b) shows

the corresponding mode in dl-methionine. The vibration is mainly localized on the nitrogen and two oxygens, and a smaller contribution from C5 and C6 . The mid-chain carbons (C3 and C4 ) are less involved in this mode. This explains why the mode only slightly shifts in resonance frequency when the fth carbon (C5 ) methylene unit is replaced by sulfur. The similarity in the mode character, resonance frequency and intensity strongly suggest that both modes have the same underlying physical origins. The slight dierence in frequency is caused by the dierent mass and charge distribution of the sulfur relative to the methylene unit. The resonance at 2.49 THz in

dl-methionine

is shown in Figure 5 c). Comparing this

mode with the 1.94 THz mode shown in b) clearly demonstrates that the sulfur contributes signicantly to the mode at 2.49 THz. The vibrational energy is mainly localized on the mid-chain carbons (C3 and C4 ) and the sulfur. The large contribution of the sulfur in this mode explains why it is without any counterpart in the THz spectrum of

dl-norleucine.

Replacing the sulfur with a CH2 group will result in a signicant change of the resonance strength and frequency, which in turn shifts it out of the measurement window.

10


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Conclusion In conclusion, we report experimental THz spectra of

dl-norleucine

dl-methionine.

and

These two amino acids are chemically similar, diering only at the fth carbon position, which is occupied by a CH2 in

dl-norleucine and a sulfur in dl-methionine.

The THz spec-

tra of both amino acids are also similar, however the strongest resonance feature is shifted by 80 GHz between

dl-norleucine

and

dl-methionine.

Furthermore,

exhibits a resonance at 2.49 THz, which is not observed in

dl-methionine

dl-norleucine.

also

These two char-

acteristics demonstrate that THz spectroscopy is an eective tool for distinguishing amino acids that have very similar chemical and crystallographic structures. Results of DFT calculations agree with the measured spectral data. Based on the calculated vibrations we were able to identify the origin of the higher frequency vibration in

dl-methionine and to

discuss the similarities and dierences between the two reported modes in dl-norleucine and

dl-methionine.

Acknowledgement We acknowledge nancial support from the national science foundation (NSF) under grant number: NSF CHE - CSDMA 1465085. HN acknowledges nancial support from BASF SE. The authors would like to thank Jacob Spies for helpful discussions.

Supporting Information Available The following les are available free of charge. dlnorleucine.fdf: Siesta input le, stating: used functional, potentials, convergence criteria, and solving strategy dlnorleucinsignelatom.fdf: Siesta input le for eigenvector calculation stating: used functional, potentials, convergence criteria, and solving strategy 11



Page 18 of 22

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