CuO/V2O5 hybrid nanowires for highly sensitive and selective H2S gas sensor

Vanadium pentoxide (V2O5) nanowires decorated with CuO nanoparticles on their surface have been prepared by a facile chemical route. The gas-sensing performance of the CuO/V2O5 nanohybrids has been examined against H2S, CO, and NO2 gases over a range of gas concentrations from 7 to 60 ppm and working temperatures from 100 to 400 C, and compared with that of pristine V2O5 nanowires without the decoration. The CuO/V2O5 nanohybrids exhibit a greatly enhanced sensitivity toward H2S gas selectively and are relatively indifferent to CO and NO2 gases. The gas-sensing response of the nanohybrids increases by nearly 18 times (from 1.84 to 31.86) when tested against 23 ppm of H2S gas at 220 C. The nanohybrids remain stable when detecting H2S gas for a period of two weeks. This selective enhancement is attributable to the local p–n junction formed at the interface together with the reversible chemical reaction that occurs when CuO is exposed to H2S gas at the temperature employed.

Introduction
Hydrogen sulphide (H 2 S) is a "broad-spectrum" poison, namely it is toxic to several systems in the human body, however the nerve system is most affected. Enzymes that exist in the human body are capable of detoxifying H 2 S by oxidation to harmless sulfates. However, the oxidative enzymes become overwhelmed when the H 2 S concentration exceeds a certain threshold level of about 300-350 ppm on average. 1 To avoid harmful incidents occurring, the design of commercial H 2 S gas sensors capable of detecting minute gas concentrations at ppm levels oen requires a detection level as low as 5-15 ppm under moderate working temperatures. In this regard, chemiresistor-type sensors based on one-dimensional metal oxide semiconductors (MOSs) are attractive since they are capable of providing gas-sensing ability for the stable detection of trace amounts of hazardous gases with a wide range of chemical attributes. To detect H 2 S gas specically, various MOS sensing materials such as WO 3 , SnO 2 , ZnO, In 2 O 3 and CuO have been explored. 2 The MOS sensors still suffer from major drawbacks such as cross-sensitivity, sensitivity to humidity, long-term signal driing and slow sensor response. 3 In particular, the poor selectivity remains a challenge to overcome and oen limits their practical applicability. [2][3][4] In the literature, the gas-sensing properties of onedimensional n-type vanadium pentoxide (V 2 O 5 ) has seldom been addressed, despite its promising potential in gas detection. [5][6][7][8][9][10] Liu et al. rst prepared V 2 O 5 nanobelts decorated with either Fe 2 O 3 , TiO 2 or SnO 2 nanoparticles by a hydrothermal method. 5,6 The hybrid nanobelts showed a moderately enhanced sensing response (S ¼ 2.0-3.1 at 100 ppm ethanol) when compared to the pristine V 2 O 5 nanobelts (S ¼ 1.7) at 200 C. Since then, V 2 O 5 nanostructures have been investigated as gas sensors for detecting mostly organic vapours. 7-10 Among them, Raible et al. reported a high sensitivity against organic amines such as 1-butylamine, with a detection limit as low as 30 ppb using V 2 O 5 nanobres. 7 Raj et al. chemically prepared V 2 O 5 nanostructures and found that V 2 O 5 showed a slightly improved sensitivity toward ethanol at ppm levels compared to ammonia with identical concentrations at room temperature. 8,9 Mondaferri et al. also demonstrated the sensing response against ammonia gas over a concentration range of 0.85-8.5 ppm at 200-250 C using electrospun V 2 O 5 nanobres. 10 Recently, the use of V 2 O 5 nanostructures for the detection of inorganic, hazardous gases has begun to emerge. [11][12][13] Yan et al. reported the room-temperature sensing capability of a porous silicon/V 2 O 5 nanorod composite with a selective, substantially enhanced sensitivity toward NO 2 gas at low concentrations (3 ppm). This compares favourably to that of organic gases such as ethanol, methanol and acetone with an even higher concentration (100 ppm). 11 Mane et al. prepared V 2 O 5 and Pd-decorated V 2 O 5 nanorods on glass substrates by chemical spraying and subsequent thermal treatment. 12,13 They also found an enhanced selectivity against NO 2 gas compared to other gases including NH 3 , H 2 S, CO, and SO 2 . 13 The use of V 2 O 5 nanostructures as sensors for detecting inorganic toxic gases requires more work to assess their applicability. We herein report the decoration of CuO nanoparticles onto V 2 O 5 nanowires to form hybrid nanostructures and investigate the gas sensitivity/selectivity of these nanostructures toward the toxic gases H 2 S, CO and NO 2 . The reason for selecting CuO for the hybrid structure lies in the fact that there are reports about enhanced selective sensing achieved with ptype CuO semiconductors exposed to H 2 S gas. 14-17 For the rst time, the CuO/V 2 O 5 nanohybrids have been found to exhibit highly sensitive and selective detection toward H 2 S gas at ppm levels continuously over a prolonged period of time (up to two weeks) and are relatively indifferent to CO and NO 2 gases over the moderate temperature range examined. The V 2 O 5 nanowires served as a backbone for the preparation of CuO/V 2 O 5 hybrids with decorative CuO nanoparticles. Fig. 3(a) shows that the CuO nanoparticles with a diameter of about 50 nm are well dispersed on the V 2 O 5 surface. Fig. 3(b) shows a typical TEM bright-eld image of the CuO/V 2 O 5 hybrids, in which discrete CuO nanoparticles seem to adhere onto the V 2 O 5 surface. The black dots are monoclinic CuO which was veried by TEM ( Fig. S1 in the ESI †). Fig. 3(c) displays an XRD pattern of the CuO/V 2 O 5 hybrids prepared via a deposition process, with a heat-treatment temperature of 400 C. Well-dened crystalline phases have been found for the orthorhombic V 2 O 5 and monoclinic CuO (JCPDS no. 48-1548), without the formation of any intermediate alloying compounds. It is worthwhile to note that the heat-treatment temperature turned out to be critically important for the successful preparation of CuO/V 2 O 5 hybrids. If the temperature was raised to 500 C, the hybrids became irregular fragments as shown in Fig. 3(d), suggesting that the V 2 O 5 nanowires had partially melted or soened (note that the melting temperature of pure bulk V 2 O 5 is about 690 C) so the structure of the hybrid was destroyed. Fig. 4 shows the sensing response of the pristine V 2 O 5 and the CuO/V 2 O 5 hybrid nanowires against 23 ppm H 2 S gas over a temperature range from 100 to 380 C. Two important ndings have been observed. Firstly, the bell-shaped distribution reveals an optimum working temperature at which the sensing response is highest. This bell-shaped temperature dependence is ascribed to two main reasons. 17 On the one hand, the adsorption, desorption and diffusion reactions involved, between the target gas and the semiconducting oxide surface, are all thermally activated processes. Hence the response increases with the working temperature. 3 On the other hand, electrons in oxide semiconductors are more likely to attain sufficient energy to jump to the conduction band from the valence band at elevated temperatures. This leads to an increased concentration of free electrons so that electrical resistance is reduced accordingly. A combination of the thermally activated process, together with the increased probability of free-electron formation as the temperature was increased, results in an optimal temperature at which the electrical resistance (and hence the sensing response) is highest. In this regard, we have demonstrated for the rst time that the optimal sensing temperature can be tailored to a lower temperature, against the model H 2 S gas at ppm levels, through the decoration  of CuO nanoparticles onto V 2 O 5 nanowires in Fig. 4. Secondly, we have found that the CuO/V 2 O 5 hybrids show a response as high as 31.86 against H 2 S gas at ppm levels at 220 C. For the rst time, this compares favourably with that of the pristine V 2 O 5 , for which the highest response is merely 1.84 at 300 C. The increased sensitivity is ascribed to the hybridization of V 2 O 5 with the CuO nanoparticles together with the decorative hybrid structure, and will be discussed in later sections.

Results and discussion
The CuO/V 2 O 5 hybrid nanowires also display a signicantly enhanced gas selectivity which is highly desirable in practical sensing applications. To illustrate this, the dynamic resistance behaviour of the pristine V 2 O 5 nanowires is displayed in Fig. 5 against H 2 S, CO, and NO 2 gases at 300 C. Responses of the V 2 O 5 nanowires are 1.84 for 23 ppm H 2 S gas, 1.48 for 60 ppm CO gas and 1.46 for 30 ppm NO 2 gas.
In addition, the response times toward detection of H 2 S, CO, and NO 2 gases are 196, 174, and 212 s, respectively, as shown in Fig. 6(a-c), for the above gas concentrations. The sensing properties are primarily ascribed to the exchange of charge carriers between the adsorbed gas molecules and the V 2 O 5 surface. In an air atmosphere, chemisorbed oxygen species, such as O 2À , O À and O 2 À , trap electrons from the conduction band of the n-type V 2 O 5 semiconductor, resulting in a spacecharge depletion near the surface. 18 Aer the introduction of the reducing H 2 S or CO gas into the testing chamber, the gas molecules would react with the previously chemisorbed oxygen  ions, so that the electrons trapped by the absorbed oxygen would subsequently be released into the bulk V 2 O 5 nanowires, according to the following reactions (1) and (2): This produces free electrons and hence decreases the electrical resistance. When the reducing gases were removed from the atmosphere, oxygen molecules spontaneously adsorb onto the V 2 O 5 surface reversibly to trap free electrons, which causes the electrical resistance to increase, returning back to its initial value. In contrast, the adsorption of oxidizing NO 2 gas would  deplete the number of charge carriers in the surface layer of the V 2 O 5 nanowires. This widens the depletion region, resulting in an increase in the electrical resistance accordingly. The desorption of gas molecules from the pristine V 2 O 5 appears to be more difficult than the adsorption, so that a "tail" was found in Fig. 6(a-c).
In addition, Fig. 5(d) summarizes the sensing response of the pristine V 2 O 5 nanowires. The lack of gas selectivity is apparent, however the sensor does provide a decent response to a change in concentration of the target gases over ppm concentrations, examined at the given working temperature. Fig. 7 shows the dynamic resistance change of the CuO/V 2 O 5 hybrids against H 2 S, CO, and NO 2 gases. The responses of the hybrids are 1.33 against 60 ppm CO gas, and 1.29 against 30 ppm NO 2 gas at 220 C. The result resembles that of the pristine V 2 O 5 nanowires at 300 C, despite the fact that the sensing temperature employed was reduced. A signicantly enhanced sensing performance was found for the CuO/V 2 O 5 hybrids toward H 2 S gas selectively. Fig. 7(a) shows the resistance change of the CuO/V 2 O 5 hybrids against H 2 S gas of various concentrations at 220 C; the responses are 31.86 at 23 ppm, 20.89 at 15 ppm and 7.86 at 7 ppm. This result indicates a dramatic enhancement of the sensing response from 1.84 for the pristine V 2 O 5 nanowires to 31.86 for the CuO/V 2 O 5 hybrids upon exposure to 23 ppm H 2 S. Compared to the rather indifferent sensitivity of the hybrid nanowires against CO and NO 2 gases, a signicantly increased sensing performance, nearly 18 times that of the pristine V 2 O 5 nanowires, has been discovered toward H 2 S gas selectively over the various gases and gas concentrations examined, as summarized in Fig. 8. Not to mention the fact that this occurs at a slightly lower working temperature (220 C). In addition, Fig. 6(d) shows that the response time of the hybrid is 130 s for H 2 S gas at a 23 ppm concentration. Therefore, the enhanced selective sensitivity is obtained with a simultaneously shortened response time. In comparison, the response times to detect CO and NO 2 gases are 268 and 211 s for the hybrids, respectively, which are similar to that of the pristine counterpart. Similar results have been found for the recovery times. The detection limit of the hybrid CuO/ V 2 O 5 nanowires has been determined experimentally, in which no response was detectable when the H 2 S concentration was below 3 ppm.
The selective enhancement and increased sensitivity toward H 2 S gas sensing of the CuO/V 2 O 5 hybrids may be explained by the p-n junction formed at the dissimilar interface and  sulfuration of the decorative CuO. The intrinsic V 2 O 5 and CuO are n-and p-type semiconductors, respectively. The decoration of CuO onto V 2 O 5 in the hybrids forms local p-n junctions at the interface. [14][15][16][17]19,20 The width of the space-charge region (W) at the interface can be estimated from eqn (3) and (4) for n-V 2 O 5 and p-CuO, respectively: 20,21 where 3 is the permittivity (2.25 Â 10 À11 F m À1 for V 2 O 5 and 2.123 Â 10 À10 F m À1 for CuO), 20,22 V o (¼ 0.6 eV) is the contact potential which is equal to the amount of the energy band bending between V 2 O 5 and CuO (f CuO À f V 2 O 5 ), q is the electrical charge of the carrier (1.6 Â 10 À19 C), and N is the carrier concentration (N V 2 O 5 ¼ 1.48 Â 10 18 cm À3 and N CuO ¼ 1 Â 10 19 cm À3 , at room temperature). 20,23 The calculated spacecharge widths are 9.97 nm for V 2 O 5 and 4.53 nm for CuO. These estimates are used for the plot of the energy-band diagram of CuO/V 2 O 5 p-n junction in air and H 2 S, in Fig. 9(a). Energy-band bending at the interface is apparent. The band gap (E g ), electron affinity (c) and work function (f) of V 2 O 5 are 2.3, 3.99, and 4.7 eV, respectively. 24,25 Those of CuO are 1.35, 4.07, and 5.3 eV, respectively. 20 Note that the calculated space-charge widths are an estimate since the carrier concentrations used in the calculation are the values at room temperature. A more precise determination of the W V 2 O 5 and W CuO needs information about the carrier concentrations at the working temperature (220 C) employed. Nonetheless, the electrical transport channel is suppressed by the presence of local p-n junctions, according to the estimates of the space-charge region. This would hence lead to a higher base resistance (as observed in Fig. 6 where the base resistance values of the CuO/V 2 O 5 hybrids were 10 to 20 times greater than that of the pristine V 2 O 5 ) and a larger change in electrical resistance (and hence sensing response) for the CuO/V 2 O 5 hybrid nanowires compared to that of the pristine V 2 O 5 counterpart.
An energy-band diagram shown in Fig. 9(b) further demonstrates how the sulfuration of the decorative CuO affects the response and recovery processes at the p-n junctions in the hybrids. In an air atmosphere, the potential barrier at the p-n junction impedes the electron ow through the interface. When H 2 S gas is introduced into the testing chamber with a concentration exceeding a certain critical level (about 7 ppm determined experimentally in the present study), the CuO is spontaneously converted to CuS by the following chemical reaction: [14][15][16] CuO + H 2 S / CuS + H 2 O CuS is a metallic conductor, thus, the p-n junction as well as the charge-depletion region transform into a metal-n-type heterostructure. The potential barrier at the p-n junction is then expected to be lowered; therefore, the conversion from CuO to CuS facilitates the electron ow, leading to the drastic decrease in the electrical resistance. Aer the inow of H 2 S gas is terminated and air is re-introduced into the chamber, CuS changes back to CuO by oxidation: The electrical resistance accordingly returns to its initial level. It may be interesting to note that the V 2 O 5 surface, without being decorated by the CuO nanoparticles as in the CuO/V 2 O 5 hybrid, may also be involved in the gas sensing when H 2 S is introduced. As yet, this appears not to contribute substantially to the H 2 S selectivity.
The gas-sensing stability of the CuO/V 2 O 5 nanohybrids has been examined against 15 ppm H 2 S for a long period of time. In Fig. 10, the sensing response remains relatively stable with an average sensitivity of 21.1 during the continuous two-week measurement. Note that every response value is in fact an average of seven measurements (as shown in the inset for the rst data point). This nding indicates that the CuO/V 2 O 5 nanohybrids may be used in practical sensing applications for the selective detection of hazardous H 2 S gas, despite more work being required to elucidate the applicability.

A. Materials
CuO-functionalized V 2 O 5 nanowires were prepared by a facile two-step route, involving hydrothermal and wet-deposition processes. In the hydrothermal process, crystalline V 2 O 5 nanowires were synthesized from a solution mixture consisting of 0.285 g V 2 O 5 powder in 9 ml de-ionized water, with dropwise addition of 1 ml hydrogen peroxide (35%) under vigorous agitation for 1 h. The solution was then placed in a Teon-lined stainless-steel autoclave and kept at 180 C for 24 h before being cooled down to room temperature naturally. The resultant V 2 O 5 nanowires were washed repeatedly with de-ionized water, centrifuged and then dried at 80 C. In the wet-deposition process, the as-prepared V 2 O 5 nanowires were dispersed in a mixed solution consisting of 10 ml of ethanol and 0.06 g of Cu(NO 3 ) 2 $3H 2 O. The suspension was then heated to 80 C for the removal of ethanol. The powder was then placed in an alumina boat and fed into the centre of a three-zone horizontal quartz-tube furnace. The tube was rst evacuated until the pressure inside reached 6 Â 10 À2 torr, before the introduction of a gaseous mixture containing 85 sccm argon (standard cubic centimetres per min at STP) and 15 sccm oxygen. The temperature was then increased to 400 C with a heating rate of 20 C per min and held isothermally for 1 h with a continuous ow of the mixed gas during the entire heating process to prepare CuO nanoparticles decorated on V 2 O 5 nanowires.

B. Characterization
The morphology and crystalline structure of the V 2 O 5 and CuO/ V 2 O 5 hybrid nanowires were examined by eld-emission scanning electron microscopy (FE-SEM), X-ray diffractometry (XRD) with Cu Ka radiation (l ¼ 0.15405 nm) and transmission electron microscopy (TEM).

C. Fabrication of the gas sensing devices
The gas sensors were fabricated by mixing the CuO/V 2 O 5 hybrids or pristine V 2 O 5 nanowires with methanol. The suspensions were then dispensed on alumina substrates with pre-congured, inter-digitated Ag electrodes. Analysis of the sensing properties was carried out in a self-assembled tubular furnace system along with a mass-ow controller, so that the concentration of various gases including air, H 2 S, CO and NO 2 gases, could be precisely tuned. The electrical resistance was recorded by a volt-amperometric Keithley 2410 every 1 s over a wide range of gas concentrations (7 to 60 ppm) and working temperatures (100 to 400 C) against target gases such as H 2 S, CO and NO 2 . For each test, the nanowire sensor was stabilized in air for 10 min before the target gas was introduced into the reaction chamber. The gas response (S) is dened as the ratio of the electrical resistance measured in fresh air (R a ) to the resistance measured in the presence of target gas (R g ). Either R a /R g or R g /R a was used for the determination of S, depending on the oxidising or reducing target gas used. The response time and recovery time are dened herein as the time it takes for the sensor to achieve 90% of its equilibrium level for the entire resistance change for adsorption and desorption of the target gas, respectively.

Conclusion
Hybrid p-CuO/n-V 2 O 5 nanowires were prepared via a facile chemical route and their gas-sensing properties were investigated. The formation of local p-n junctions at the nanometre scale CuO/V 2 O 5 interface, together with the reversible sulfuric/ oxidative reactivity when exposed to cyclic H 2 S gas/air at moderate temperatures, signicantly enhanced the response and selectivity toward H 2 S gas sensing. The hybrid nanowires showed a rather indifferent response when CO and NO 2 were used as the target gas. This unique selectivity toward H 2 S gas at precise ppm levels means that hybrid p-CuO/n-V 2 O 5 nanowires are anticipated to be used in a stable and reliable sensing device suitable for practical alarm applications.

Conflicts of interest
There are no conicts to declare.


extfieldsofstudy: Medicine Physics Biology Chemistry

s2fieldsofstudy: Chemistry Biology

text:
Deciphering Intrinsic Inter-subunit Couplings that Lead to Sequential Hydrolysis of F1-ATPase Ring

Rotary sequential hydrolysis of the metabolic machine F1-ATPase is a prominent manifestation of high coordination among multiple chemical sites in ring-shaped molecular machines, and it is also functionally essential for F1 to tightly couple chemical reactions and central γ-shaft rotation. High-speed AFM experiments have identified that sequential hydrolysis is maintained in the F1 stator ring even in the absence of the γ-rotor. To explore the origins of intrinsic sequential performance, we computationally investigated essential inter-subunit couplings on the hexameric ring of mitochondrial and bacterial F1. We first reproduced in stochastic Monte Carlo simulations the experimentally determined sequential hydrolysis schemes by kinetically imposing inter-subunit couplings and following subsequent tri-site ATP hydrolysis cycles on the F1 ring. We found that the key couplings to support the sequential hydrolysis are those that accelerate neighbor-site ADP and Pi release upon a certain ATP binding or hydrolysis reaction. The kinetically identified couplings were then examined in atomistic molecular dynamics simulations at a coarse-grained level to reveal the underlying structural mechanisms. To do that, we enforced targeted conformational changes of ATP binding or hydrolysis to one chemical site on the F1 ring and monitored the ensuing conformational responses of the neighboring sites using structure-based simulations. Notably, we found asymmetrical neighbor-site opening that facilitates ADP release upon enforced ATP binding. We also captured a complete charge-hopping process of the Pi release subsequent to enforced ATP hydrolysis in the neighbor site, confirming recent single-molecule analyses with regard to the role of ATP hydrolysis in F1. Our studies therefore elucidate both the coordinated chemical kinetics and structural dynamics mechanisms underpinning the sequential operation of the F1 ring.

INTRODUCTION
Coordination on ring-shaped NTPases is fundamental and crucial for the diverse physiological functions of these cellular molecular machines (1)(2)(3)(4)(5). In well-studied systems such as F o F 1 -ATP synthase, the binding-change mechanism, for example, was proposed early on to illustrate rotary cooperative catalysis around the hexameric F 1 -ATPase ring (6,7). The mechanism indicated that binding and catalytic activities of ATP alternate sequentially on three chemically active sites, formed at the interfaces of the a and b subunits on the ring (8). According to the mechanism, the central g-shaft across the F 1 ring dictates the coordinated alternation (9)(10)(11)(12). Nevertheless, experimental studies later on showed that upon significant truncations of the g-shaft, the F 1 motor still rotates directionally (13)(14)(15)(16). Furthermore, recent experiments conducted in the absence of the central g-shaft demonstrated that the stator F 1 -ring also maintains rotary sequential hydrolysis around the three chemical sites (17). These studies consistently indicated that the sequential coordination arises intrinsically from the F 1 -ATPase ring, though the stator-rotor interactions would likely enhance the rotary cooperativity.
In this work, we aimed to investigate how the intrinsic sequential operation on the F 1 ring arises due to inter-subunit or site couplings in the absence of the central g-shaft.
We assume that the sequential hydrolysis scheme achieved without the g-rotor is similar to that detected originally with the rotor. We focused on two typical reaction schemes, one suggested recently for human mitochondrial F 1 (MF 1 ) (18), and the other determined for bacterial F 1 (BF 1 ) (19). For an individual ATPase site, formed by one a-b heterodimer, the uni-site reaction rates for the product ADP and Pi releases, for example, are particularly low (20,21). To allow reactions that are as fast as that achieved on the trisite F 1 ring, it is necessary that the inter-subunit couplings significantly accelerate the respective product releases, yet how that is achieved remains elusive. Inter-subunit coordination has been recognized in particular for ring-like NTPases (1,2,22), such as the viral RNA or DNA packaging motor (23,24), helicases (4,5,25), and F 1 -ATPase (2,6,26). For example, in the viral f29 DNA packaging motor, it was discovered that multiple subunits coordinate ADP release with ATP binding in an alternating fashion during a packaging dwell phase (1,24,27), whereas Pi release happens from one site to the next in a burst phase. Nevertheless, it is not clear what inter-subunit interactions support the coordination, and similar puzzles remain for various ringshaped NTPases. Some suggestions have been made that address, for example, how ATP binding in one site may couple with ADP release in a neighbor site (1,24,26,27), how an arginine-finger insertion from one subunit can induce ATP hydrolysis in the next-neighbor site (23,24,27), and how ATP hydrolysis may assist Pi release in the neighbor site (28) or vice versa. A basic scenario is that one chemical event triggers certain conformational changes that propagate through the subunit interfaces to the neighbor site(s), accelerating the site conformational transitions on the forward chemical reaction path, with both kinetic and structural consequences. However, quantitative studies to reveal these couplings and determine the underlying kinetics or structural dynamics are lacking. Accordingly, the major task of this study is to identify the inter-subunit couplings that essentially support the sequential hydrolysis of the F 1 stator ring, along with quantitative descriptions and physical understanding. Computational modeling and simulations have contributed significantly to the understanding of molecular mechanisms of F 1 -ATPase (29)(30)(31)(32)(33)(34)(35)(36)(37)(38). Although most previous computational studies have focused on quantifying the rotary motion of F 1 -ATPase (a 3 b 3 g), current work has neglected the rotational degree of freedom and studied only a minimal model of the F 1 ring (a 3 b 3 ) for sequential hydrolysis. We started by conducting stochastic kinetics simulations for the three independent ATP hydrolysis cycles, based on the uni-site reaction rates obtained for bovine heart MF 1 (21) and Escherichia coli F 1 (20). Empirically chosen inter-site couplings that are likely to happen upon assembly and operation of the ring were then kinetically incorporated into the stochastic simulation, and the kinetic rates were tuned, in particular, under a constant free-energy condition for ring operation. If a sequential hydrolysis reaction arises in the tri-site reaction as experimentally detected under these couplings, we then regard the couplings as kinetically feasible.
For the kinetically feasible inter-subunit couplings that were identified as key for sequential hydrolysis, we then probed the physical basis of the couplings with structural dynamics investigations. Previously, atomistic molecular dynamics (MD) simulation studies had been performed on the F 1 -ATPase system to reveal protein conformation changes from several nanoseconds (30) to tens and hundreds of nanoseconds (37). Nevertheless, micro-to millisecond ''long-timescale'' dynamics in such a protein machine is still hardly accessible for conventional MD simulations. As mentioned above, the inter-subunit couplings are usually manifested as the neighbor-site conformational responses toward an active site where some triggering chemical event, such as ATP binding or hydrolysis, happens, with a ''waiting time'' up to milliseconds or above. To allow such a ''slow'' event to happen in the MD simulation, we accordingly enforced conformational transitions to mimic the ATP binding or hydrolysis event in the corresponding active site by implementing targeted MD (TMD) in sub-microseconds (39)(40)(41). However, the purpose is not to simulate the triggering event per se, but to monitor the ensuing conformational relaxations or responses on the ring. Considering that artifacts or bias might be introduced in the highly accelerated sub-microsecond TMD, we additionally performed coarse-grained (CG) simulations with similar enforcing and relaxation strategies, since CG simulations are supposed to capture comparatively slow motions. As the essential conformational responses appearing in the accelerated atomistic MD simulation could be reproduced on the CG level connecting to the long timescale, the TMD-induced responses are regarded to be as reasonable as those that happen without acceleration.
In practice, we adopted a reaction scenario in which Pi is released after the ADP release in one hydrolysis cycle of F 1 (19,42). Using stochastic kinetic simulations, we were able to first determine kinetically feasible inter-subunit couplings that support the sequential hydrolysis. Then, we implemented atomistic MD simulations to probe the physical basis of the kinetically important couplings. The bovine MF 1 structure was employed in the MD simulation. Once the TMD was implemented to mimic ATP binding or hydrolysis in one active site, the conformational responses in both neighbor sites were closely monitored. We subsequently found asymmetrical neighbor-site openings that may facilitate the product(s) release or bias the ATP binding for directional coordination. To validate the TMD implementation to a comparatively long timescale, we further implemented targeted elastic network (TEN) simulations in a CG structural model.

Kinetic Monte Carlo simulation of three chemical sites
For each ATP binding or catalytic site at the a-b interface, there are several chemical states: the empty state without any substrate binding (E); the ATPbound state and the hydrolysis-ready state (T/T*); the post-hydrolysis state right after the reaction, as ATP turns into ADP and Pi (DP); and the ADPreleased but Pi-bound state (P). Here, we follow the convention that the ADP releases before the Pi release (19,42). As such, the uni-site reaction proceeds in cycles as E5T/T*5DP5P5E. We differentiate T* from T by enhancing the ATP-hydrolysis rate of the T*-state above that of the T-state, as if T* arises due to the assembly of the tri-site ring.
The uni-site reaction rates for forward and backward transitions in the bovine heart mitochondrial and bacterial E. coli F 1 -ATPase were obtained experimentally (20,21) (see Tables S1 and S2). We assume that the rate of ADP release from the DP state is the same as that originally listed from the D state, and the rate of Pi release from the P state is the same as that originally listed from the DP state. We also assume that bovine and human MF 1 behave similarly (18), and that E. coli and thermophilic (Bacillus PS3) BF 1 perform alike as well (43).
We used the kinetic Monte Carlo (KMC) method (44) to simulate the chemical kinetics of F 1 -ATPase hydrolysis, from the three independent uni-site reactions to the coupled tri-site reactions. In the KMC simulation, one starts with an initial ring configuration (e.g., E-E-E or E-DP-T) of the three chemical sites; each time a transition from one of the three chemical sites was made, either forward or backward along the reaction path, according to rate competitions of all potential transitions in the current ring configuration (i.e., fast transitions get higher chances). When the uni-site reaction rates were adopted for each site, the three sites performed as if they hydrolyzed independently. In any coupled tri-site reaction scheme, inter-subunit couplings were imposed at certain ring configurations, for example, by tuning the product-release rates upon neighbor-site ATP binding (E/T) or hydrolysis reaction (T*/DP). In particular, we used four parameters to define the strength of the couplings, and we tuned these parameters for optimal sequential performance (see the Supporting Material).

Atomistic TMD simulations
All the MD simulations were performed using the NAMD 2.10 software (45) with the CHARMM22 force field for protein and the CHARMM27 force field for lipid (46,47), except for the construction of the E-DP-T structure, for which GROMACS was used (48). The F 1 -ATPase structures were obtained from the existing crystal structures: The E-DP-T ring was made from the crystal structure of P-DP-T (Protein Data Bank (PDB): 1E1R) (49); the g-shaft, when included, was rotated $40 accordingly. An E-T-T* structure was obtained directly from the crystal structure (PDB: 2JDI) (50). An E-E-E structure was made from E-T-T, and a T-P-T* structure was obtained from the crystal structure (PDB: 1W0J) (51) (see the Supporting Material).
The PDB structures were then solvated with TIP3P water in a cubic box, and the minimum distance from the protein to the wall was 15 Å . We neutralized the systems with Na þ and Cl À to a concentration of 0.15 M. The temperature was set to 310 K and the pressure was 1 bar. The van der Waals and short-range electrostatic interactions used a cutoff of 12 Å . The particle-mesh Ewald method was applied to deal with long-range electrostatic interactions (52). The solvated system was minimized with the steepest-descent algorithm, followed by a 10 ps MD simulation under the canonical ensemble with a time step of 1 fs. Then, a 5 ns equilibrium simulation was performed under the NVT ensemble with a time step of 1 fs, and position restraints were imposed on the heavy atoms of proteins during the simulation. After the constrained simulation, the unconstrained equilibrium simulations, or TMD simulations, were carried out under the NPT ensemble with a time step of 2 fs. During the TMD simulation, the structure was constantly forced toward a moving target conformation (according to the heavy-atom root mean-square deviation (RMSD) value) geometrically designated on the reaction path toward a final target structure (39). Further implementations are found in the Supporting Material.

Performing the elastic-network relaxation dynamics
The elastic network of the ring was obtained by first replacing each amino acid residue in the atomic structure by a single bead, which was placed at the position of the a-carbon atom of the respective residue. These equilibrium positions were denoted byR ð0Þ i for bead i. Then, to determine the pattern of network connections, the distances d j between equilibrium positions of any two beads i and j were compared with a prescribed interaction radius r int ¼ 10 A. If this distance was below r int , the two beads were connected by a deformable elastic spring with natural length d ij . The network connectivity was stored in matrix A with entries A ij ¼ 1, if beads i and j are connected, and A ij ¼ 0, else. The total elastic energy of the network is U ¼ Here, N is the number of beads in the protein network, d ij ¼ R i ÀR j is the actual length of a spring connecting beads i and j in some deformed network conformation, withR i being the actual position vector of bead i, and d ij is the corresponding natural length. The spring stiffness constant k is assumed to be the same for all network springs.
When thermal fluctuations and hydrodynamical interactions are neglected, the dynamics of the network can be described by a set of Newton's equations in the over-damped limit (53)(54)(55). For bead i the equation of motion is On the left side of Eq. 1, g is the friction coefficient assumed to be equal for all network beads. On the right side are the elastic forces exerted by network springs of beads which are connected to bead i. Explicitly, the equations read Here, we have removed the dependencies on g and k by an appropriate rescaling of time and, after that, added external forcesf i which can act on bead i (if s ¼ 1).
In the TEN simulations performed, external forces were applied only to the beads of one of the catalytic ab -sites to induce the desired transition there. Such forces were updated in each integration step and had the formf i;n ¼ ða=N s ÞjRMSD nÀ1 À RMSD Ã jd i;nÀ1 , for bead i. Here,d i;n is the difference vector between positions of bead i in the target and the actual conformation of the forced ab -subunit, determined after superposition of the subunits at integration step n, and RMSD Ã ¼ RMSD 0 À RMSD 0 ðn=SÞ, with S being the total number of integration steps. N s is the number of beads of the forced ab -subunit, and parameters a ¼ 2500 and S ¼ 400; 000 were chosen in the simulations. The set of Eq. 2 was numerically integrated to obtain the positions of network beads at all moments in time. In the simulations, a first-order scheme with a time step of 0.1 was used. In particular, we performed TEN to mimic ATP binding to the E-site of the E-DP-T ring, in comparison with the TMD simulation. Further details can be found in the Supporting Material.

Stochastic simulations identified kinetically feasible inter-subunit couplings that support sequential hydrolysis on the F 1 ring
To probe what type of inter-subunit or site couplings may be responsible for sequential hydrolysis of the F 1 ring, we first conducted the kinetic Monte Carlo (KMC) simulations for three ATP hydrolysis cycles to mimic the chemical kinetics of the three active sites (see Fig. 1; Methods). The three chemical cycles proceed independently when there is no inter-subunit coupling. The coordinated sequential hydrolysis arises kinetically when certain transitions in one hydrolysis cycle are connected with those in another hydrolysis cycle at the right moments via appropriate coupling rules (see Supporting Material).
We started by simulating the three independent hydrolysis cycles based on the uni-site reaction rates obtained experimentally, for both MF 1 and BF 1 (20,21) (see Tables S1 and S2). Each hydrolysis cycle consists of ATP binding (from E, the empty state, to T, the ATP-bound state), hydrolysis (T or T* to DP, the ADPþPi bound state), and product release (DP to P, the Pi-bound state, and then to E). We then imposed coupling rules onto the three ATP hydrolysis cycles in the KMC simulations (Fig. S1). First, since the three-ATP-bound configuration (3-T) was not detected experimentally (17), we imposed a constraint to prevent 3-T when needed by lowering the third ATP binding rate to the ring (e.g., for $100 times the rate inhibition; see Figs. S1, S2, and S3). It turns out that MF 1 explicitly requires the constraint to achieve the sequential performance, since on the dominant reaction path of MF 1 (see Fig. 1 B), a T-E-T* configuration exists that readily turns into 3-T, which can then obtain a large population in the absence of the constraint (e.g., >60%). In BF 1 , however, the sequential performance was acceptable without adding the constraint, and the 3-T population would not become dominant (i.e., it remained at <30%). Second, when two sites among the three are bound with ATP, we refer to the T*-site as the one that binds ATP earlier, so that it proceeds to an intermediate T* state (or tightly bound state, as in the assembled ring), ready for catalysis (31). We accordingly assigned an elevated ATP hydrolysis rate (e.g., $100-fold rate enhancement; see Figs. S1, S2, S3, and S4) for the T*-site.
Note that sequential performance was evaluated by a performance score (between 0 and 1), according to the experimentally detected sequential schemes (18,19). A higher score shows a better sequential performance or consistency with the detected scheme (see Eq. S1 in Supporting Materials and Methods; Figs. S2, S3, and S4). In the case of a high score, one can consistently see high correlations between neighboring sites in their hydrolysis cycles, as one site follows the other closely moving along the hydrolysis reaction path (see Eq. S2 in Supporting Materials and Methods; Fig. S5).
Representative trajectories for the ATP hydrolysis cycles on the three active sites of the BF 1 ring are shown in Fig. 1 A, from an independent case to a partially coordinated and then a highly sequential case. In particular, the highly sequential case demonstrates an overall cycling rate ($0.3 s À1 ) comparable to the experimental detection on the rotor-less BF 1 (17). In the full F 1 in the presence of the central rotor, the cycling rates become hundreds to thousands times faster (18,43).
Since it is not clear whether product binding affinities change during the inter-subunit coupling, we imposed the coupling kinetically in two ways (see Fig. 1 A, right): For implementation I, we enhanced both the product unbinding and binding rates by the same amount to keep a constant binding affinity. For implementation II, we enhanced the product unbinding rate without changing the product rebinding rate, whereas the ATP unbinding rate or the reversal rate of the hydrolysis in the triggering active site was additionally enhanced to keep the overall free energy constant. The trajectories for MF 1 and BF 1 with both implementations I and II are shown in Fig. S6. Regardless of the means of implementation, we found that the key couplings that support the sequential schemes are the same as those summarized below.
ATP binding to the E-DP-T ring facilitates product release from the downstream DP site Presumably, as ATP binding (E/T) induces an open-toclosed transition in the E-site, the next downstream DP-site (in the counterclockwise direction viewed from the C-terminal side of F 1 ) can be disturbed and the product (ADP and Pi) release rate can be affected (1,24,26). Accordingly, in the FIGURE 1 Stochastic simulations of tri-site hydrolysis reactions on the F 1 ring. (A) The trajectories (left) show the number of hydrolysis cycles for the three chemical sites of BF 1 , from the independent (yellow traces, with three different shades shown for the three active sites) to the partially coordinated (blue traces with three shades) and the highly sequential case (red traces with three shades). In the sequential case, each site follows its upstream/counterclockwise site along the ATP hydrolysis reaction path, as detected experimentally. In the independent case, the uni-site reaction rates from E. coli F 1 were used (20). The ring-shaped structure (right) of a key configuration, E-DP-T, is shown (E for the empty state, T for the ATP bound state, DP for the ADP*Pi or the hydrolysis state, and P for the Pi bound state), with the most essential inter-subunit coupling illustrated: ATP binding to the E-site facilitates ADP release from the next DP-site. The coupling is imposed in two ways, implementations I and II (see text). Implementation I was used for the BF 1 trajectories shown here. (B) The sequential hydrolysis schemes for MF 1 (top) and BF 1 (bottom), with the essential inter-subunit couplings enabling the schemes indicated. The ATP binding (E/T) to E-DP-T enhances the ADP release (DP/P) for both MF 1 and BF 1 ; in MF 1 , Pi release (P/E) is enhanced right after the ADP release upon ATP binding, whereas in BF 1 , Pi release is enhanced either similarly to that in MF 1 and/or later, upon ATP hydrolysis (T*/DP). To see this figure in color, go online. kinetic simulation, we allowed the ATP binding to the E-DP-T ring to enhance both the ADP and Pi release rates in the DP-site. In MF 1 , >$10 5 -fold rate enhancement (see Fig. S3) was applied to both the ADP and Pi release (from E-DP-T to T-E-T*) to achieve a high sequential performance. In BF 1 (from E-DP-T to T-P-DP), the ADP release rate has to be enhanced > 10 3 -fold upon the E-site ATP binding (see Fig. S4) to allow the sequential performance; the Pi release rate either can be enhanced along with ADP release upon ATP binding or can occur after T*-site ATP hydrolysis (see Fig. S2, B and C), as analyzed below.
The Pi release from the T-P-T* ring can be facilitated either by the upstream-site ATP binding or later by the downstreamsite ATP hydrolysis Based on time-series data analyses from high-speed singlemolecule experiments, it was suggested that ATP hydrolysis plays a role in facilitating the neighbor-site Pi release (28). We tested whether this causality coupling between ATP hydrolysis and Pi release could be kinetically feasible, i.e., to support sequential hydrolysis in the KMC simulation. We then found that in BF 1 , by enhancing the Pi release rate $10 3 -fold upon ATP hydrolysis in the next T*-site (see Fig. S4), sequential hydrolysis could emerge. Alternatively, Pi release in BF 1 can also be enhanced right after ADP release, as in MF 1 , to support the sequential performance.
Note that the overall hydrolysis or cycling rates of F 1 achieved in our KMC simulations are comparatively low, e.g., less than one cycle (with three ATPs hydrolyzed) per second, as experimentally detected for BF 1 in the absence of the rotor (17). One can also enhance the coupling strengths to mimic the full F 1 system in the presence of the rotor to achieve high rates, i.e., up to hundreds of cycles per second, as measured for the full F 1 (18,43). The corresponding kinetic coupling parameters to achieve the low and high rates of F 1 are provided in Tables S3 and S4 for MF 1 and BF 1 , respectively.
In brief, from a kinetic perspective, the ATP-bindingfacilitated ADP release in the downstream DP-site appears to be an indispensable coupling for sequential performance for both the MF 1 and BF 1 rings. On the other hand, the coupling for promoting Pi release could be attributed either to ATP binding in the upstream site (in MF 1 ), or to ATP hydrolysis in the downstream T*-site, or both (in BF 1 ). To further probe the physical basis of these kinetically feasible couplings, we performed atomistic MD simulations as illustrated below.
Atomistic MD simulations demonstrated an asymmetrical opening of the neighbor site upon current-site closing/tightening induced by ATP binding/hydrolysis We performed four sets of TMD simulations (39) mimicking ATP binding or ATP hydrolysis in one chemical site, and we monitored the ensuing mechanical responses from the two neighboring chemical sites. The four sets of simulations include 1) targeting the ATP-binding transition from E-DP-T to T-DP-T* to examine how the downstream DPsite and the upstream T-site are affected, with a control TMD simulation to include the central g-shaft; 2) targeting the ATP hydrolysis transition from T-P-T* to T-P-DP to examine how the upstream P-site and downstream T-site react; 3) targeting the first-ATP binding transition from E-E-E to E-T-E to examine the responses without ligand bound in the neighbor sites; and 4) targeting the third-ATP binding transition to E-T*-T, to see if the 3-T ring remains stable.
ATP binding to the E-DP-T ring opens the downstream DP-site to facilitate ADP release We obtained an E-DP-T ring from the P-DP-T structure of bovine MF 1 (PDB: 1E1R) (49) and performed the TMD simulation to enforce the a E -b E structure to approach the targeted a T -b T conformation, so that the original E-site was turned into a T-site and a T-DP-T* ring was obtained (see Fig. 2; Supporting Material, section II.4).
To determine whether the ATP binding site transited from open to closed as it was enforced to do, we calculated the C-terminal protrusion (i.e., on the DELSEED motif) height, the hinge-bending angle on the b-subunit, and the size of the ATP binding pocket (see Fig. S7). Large values of these measures indicate an open form, whereas small values indicate a closed one. In Fig. 2 A, we see that the b E -protrusion decreased by $6 Å during the TMD simulation, indicating clearly a transition from an open site to a closed one (E/T). In response, the average b DP protrusion height increased slightly (by $1 Å ; also see Fig. 2 B) and the b DP hinge-bending angle also increased (by $3 ), accompanied by a small increase in the pocket size ($0.2 Å ; see Fig. S8), all indicating a slight opening of the DP-site compared with the results from an equilibrium control simulation. In comparison, the average b T -protrusion height decreased a little ($1 Å ), though the pocket size of the T-site increased a bit ($0.2 Å ), and the hinge-bending angle of b T increased slightly ($1 ). Movies made from the simulation show both top and side views of the ring, highlighting how the b-protrusions shifted (Movies S1 and S2).
Since the average magnitudes of the responses were small, we performed an additional TMD simulation for the control, retaining the g-shaft in the center of the E-DP-T ring. The average b DP protrusion then increased to $2 Å upon the E-site closing (see Fig. S9), whereas the pocket size only increased in the downstream site but decreased in the upstream site. In brief, all three geometric measures consistently suggested that the downstream DPsite opened in response to the ATP binding in the E-site, whereas the upstream T-site did not show such an opening tendency. In particular, one could see that the DELSEED of b E/T moved toward the center of the ring during the enforced transition (see Fig. 2 C). The trend was maintained in the presence of the g-shaft, though the g-shaft occupancy prevents the b E/T protrusion from interacting directly with that of b DP , and the b DP protrusion then increased, largely due to the g-shaft rotation.
Notably, even without the g-shaft, one still sees that the DP-site interface widens between a DP and b DP upon the enforced ATP binding (see Fig. 2 C). The conformational changes are actually quite significant in the peripheral region of the DP-site (within 10 Å of the bound ADP), with an RMSD of $3 Å upon the enforced transition (see Fig. S10 A). The average number of hydrogen bonds in that region also decreased (from $25 in the equilibrium MD to $20 in the TMD simulation; see Fig. S10 B). In particular, the hydrogen bonds that connect a DP and b DP and ones on the b-strand of a DP frequently broke in the TMD simulation, but not in the equilibrium control simulation. All these features indicate an enlarging of the DP-site interface in response to the enforced ATP binding to the E-site.
To further probe how the DP-site region was able to respond to the enforced E-site to facilitate the ADP release, we also conducted steered MD (SMD) simulations to pull ADP out of the DP-site from the initial E-DP-T ring (before the TMD) and from the final T-DP-T* structure (after the TMD), respectively. Three directions were chosen for the ADP pulling: upward from the top of the DP bound pocket, and outward from and inward to the center of the ring. Correspondingly, we conducted three SMD simulations for each direction, to both the E-DP-T and T-DP-T* rings before and after the TMD simulations (3 Â 3 Â 2 ¼ 18 SMD simulations; see Fig. S11; Supporting Material, section II.4). The results show that after the TMD simulation or the E-site closing, it was comparatively easy to pull the ADP out of the DP-site, and the contrast was made apparent for pulling along the upward and/or outside pathways. Close inspections along the steered ADP release paths show some structural clues as to how the release could possibly proceed (see Fig. S11).
Finally, we probed how the mechanical responses propagate from the ATP-binding E-site to the respective DP-and T-site in the stator F 1 -ring, without the g-shaft. We calculated individual residue correlations with the E-site ATPbinding residues (aI343, aR373, bG161-V164, bY345, bA421, bF424, and bT425), which are mainly on the b E subunit (see Fig. 3 A) by first evaluating the pairwise cross-correlation values for all residues (see Fig. S12) and then summing up the correlation strengths between each protein residue and those E-site ATP-binding residues. Close to the E-site, the correlations generated were similarly high across a E->T and b E->T , respectively (see Fig. 3 A, right). The correlation was still maintained high as being propagated from a E->T to b DP , owing to an a-loop region (aQ405-D411) on the top of a E->T that interacts closely with the DELSEED region (bD394-D400) from b DP and a helix underneath (bD383-M390). Indeed, upon ATP binding to the E-site, the a E->T -loop pushes toward the b DP helix and DELSEED region and moves slightly outward, away from the center, allowing the b DP protrusion to increase and the DP-site to slightly open. On the other hand, the propagation from b E->T to a T and to b T was over a comparatively long distance, and the correlation decayed noticeably reaching toward b T . Since the ADP/ATP binding site mainly locates on the b-subunit, it is reasonable to see that the upstream T-site was affected less than the downstream DP-site by the E-site ATP binding.

ATP hydrolysis in T-P-T* facilitates Pi release from the upstream P-site
To mimic ATP hydrolysis in the T-P-T* ring (PDB: 1W0J) (51), we enforced the T*-site to a targeted DP-site confor-mation, obtained from the crystal structure (PDB: 1E1R) (49). Interestingly, one notices that in the crystal structure of T-P-T*, the P-site Pi is located around the bP-loop, a marginally stabilized position according to a recent MD study probing the free energy of Pi release (37). It was indicated that the doubly charged Pi group has a tightly bound state located $7 Å inside, whereas the P-loop bound state is a less stabilized intermediate state close to the exit of the Pi release channel.
Since the ring structure T-P-T* is obtained from bovine MF 1 , the marginally stabilized positioning of Pi in this structure, by itself, suggests a coupling scenario consistent with our proposal for MF 1 (see Fig. S1 C): the Pi release from the P-site of T-P-T* (to T-E-T*) has been facilitated right along with the ADP release (from T-DP-T* to T-P-T*) upon ATP binding in the upstream site (E-DP-T to T-DP-T*; see Fig. 1 C, top).
Moreover, we captured in the TMD simulation of the T-P-T* ring a complete Pi release event from the P-site upstream of the enforced T*-site. Within 50 ns of the TMD simulation, the protrusion of the T*-site dropped slightly, FIGURE 3 Conformation correlation with the ATP-binding-pocket residues in the TMD simulation of the E-DP-T ring. (A) Correlation map of the full ring during the enforced E/T transition starting from E-DP-T, colored according to correlation values (blue/white/red, high/medium/low) between individual residues and the E-site ATP binding residues (green spheres in the top view on the left). An inside view (right) shows the conformation propagation or correlation from a E/T to b DP and to a DP (left), and from b E/T to a T and to b T (right), with the bound ADPþPi and ATP at the DP-site and the T-site, respectively, circled. (B) The residue-wise correlation from b DP (blue) and b T (yellow). (C) A close inspection of the C-terminal region of a E/T to b DP during the TMD simulation is shown, with cartoon schematics on the left and zoom-in structural views on the right. To see this figure in color, go online.
showing a tightening of the site key to the ATP hydrolysis (T*/DP). Meanwhile, one notices an up to $3 Å rise of the b P protrusion for the P-site (see Fig. 4 A; Fig. S13), indicating an opening response of the P-site within 50 ns that consequently led to the Pi release. The finding that the Pi release was facilitated upon the enforced hydrolysis nicely confirms the prediction from the recent experimental data analyses (28), conducted for BF 1 (thermophilic Bacillus PS3).
Remarkably, our TMD simulation demonstrated a complete charge-hopping pathway of the Pi release through three arginine residues and one lysine residue (see Fig. 4 B; Movies S3 and S4), which has not been revealed before. The Pi group was initially positioned through hydrogen bonding with both the P-loop from the b P subunit and the first arginine finger residue, Arg373, from the a P subunit. In response to the enforced hydrolysis transition, T*/DP, the P-loop from b P retracted slightly from Pi. Meanwhile, Arg143, the second arginine finger from a P , which frequently switched its side chain between Arg373 and Glu144, captured Pi after $50 ns of the simulation, so that Pi dissociated from Arg373. In addition, three negatively charged residues from the b P subunit, Asp195, Glu199, and Glu202, helped to repel Pi away from b P . Later on, Pi was further transferred to Lys196 ($140 ns) and Arg161 ($180 ns) on a P and then released fully from the To understand why the conformational transition T*/ DP impacts the P-site that is upstream to the enforced T*-site, we examined again the residue-wise correlations on the T-P-T* ring during the enforced transition (see Fig. 5). In particular, we see that the overall correlation decayed quickly right away from the T*-site. Nevertheless, one notices that the local region of the P-site correlates well with the T*-site residues. A close examination shows that the correlation propagates from the hydrolysis site on b T * /DP , via an inactive site at the interface of b T * /DP and a P , and then extends along a narrow region of a b-sheet structure in the middle part of a P (aArg164-Arg171, aIle345-Leu352, and aLeu369-Arg373), and finally reaches the P-site at a P -b P . The connection with the corresponding residues in a T * /DP was, however, broken toward the b T direction due to a gap region right at the a T * /DP -b T interface, where another inactive site is located (see Fig. 5 C). A movie was made to show the dynamics of the conformation propagation from the T*-site to the P-site (see Movie S6). The full pathway of Pi release captured in the TMD simulation. b P is colored in ice blue, its P-loop in magenta, and a P in cyan. The key charged residues are colored in blue (positively charged) and red (negatively charged). The Pi group (spheres) hopped from the arginine finger aR373 to aR143 ($80 ns), and then to aK196 ($140 ns) and aR161 ($180 ns) before the final release. Three negatively charged residues from b P (D195, E199, and E202) also helped the Pi release through repulsion. To see this figure in color, go online.

The first ATP binding opens the next downstream E-site more than the upstream E-site
To investigate whether asymmetrical responses arise on the early tri-site reaction path, we conducted the TMD simulation to a fully empty ring E-E-E (see Figs. S14 and S15; Supporting Material). First, we enforced an E/T transition on one pair of a E -b E (blue site) in the E-E-E ring; we then observed trends of mechanical responses similar to those in the E-DP-T configuration: The downstream E-site (yellow site) opened compared to the equilibrium control simulation, whereas the upstream E-site (green site) did not (see Fig. 6 A; Fig. S15). Further calculations on the cross-correlations also show an asymmetrical pattern (Fig. S16). Nevertheless, the three E-sites in the E-E-E ring were not identical (see Fig. 6; Fig. S14), e.g., one of the sites (green site) appears to open more than the other two as its protrusion height and pocket radius stay comparatively large in the equilibrium simulation. Accordingly, we conducted an additional run of the TMD simulation to see if the responses were sensitive to the initial configuration of the E-site. Again, by enforcing an E/T transition to another E-site (green site), the downstream site (now blue) opens more than the upstream site (yellow site), though one would notice that the opening bias appears small and large fluctuations are sampled in the MD simulations (see Figs. S14 and S15). Anyhow, it is also interesting to notice that the yellow E-site, being the downstream site in the first TMD run (see Fig. 6 A), demonstrated a much larger increase of the protrusion height than in the second TMD run, in which it became the upstream site of the enforced ATP binding site. Hence, we concluded that without ligand binding in the neigh-boring active sites, the asymmetrical responses toward the ATP binding already exist in the ring.
Indeed, the asymmetrical responses triggered by the first ATP binding to the ring can bring a bias in recruiting the second ATP. We found through the KMC simulation that if the second ATP is recruited to the downstream site with a slight bias over the upstream site (e.g., a binding-rate ratio of $10), then the reaction intermediate quickly converges to E-T*-T, and then to E-DP-T (see Fig. 6 C), rather than to the ''reversal configurations'' T-T*-E and then T-DP-E. Once the E-DP-T configuration is reached, the chemical cycles repeat, as demonstrated in Fig. 1 C, for both MF 1 and BF 1 .

The third ATP binding to the ring destabilizes both neighboring ATP-bound sites
In the KMC simulation, the 3-T configuration in BF 1 was absent due to the coordinated tri-site kinetic, i.e., T-T-T was simply not on the dominant reaction pathway. In contrast, the 3-T configuration in MF 1 needs to be explicitly prohibited to support sequential performance, by reducing the third ATP binding rate ($10 to 100-fold; see Fig. S3 A). In the MD simulation, nevertheless, we enforced a third ATP binding to the E-T*-T ring (i.e., an intermediate on the MF 1 reaction path) to probe the mechanical (in-)stabilities. We noticed an abnormal increase of the pocket size in the upstream T-site, even though the b T protrusion dropped (see Figs. S17 and S18). Notably, the bound ATP from the downstream T*-site released in one of the two TMD simulation trials, though the T*-site did not open significantly. Hence, the enforced third ATP binding appears unfavorable, as it triggers significant distortions or even destabilizes the bound ATP. In brief, an E-T*-T ring would FIGURE 5 Conformation correlation with the ATP hydrolysis pocket in the TMD simulation of the T-P-T* ring. (A) Correlation map (left) of the full ring during the enforced T*/DP transition starting from T-P-T*, colored according to the correlation values (blue/white/red, high/medium/low) between individual residues and the T*-site ATP binding/hydrolysis residues (green spheres). An inside side view (right) shows the conformation propagation or correlation from a T * /DP to b T to a T , and from b T * /DP to a P to b P . (B) Residuewise correlation from b P (blue) and b T (green). (C) A close structural view of the connecting residues along the two propagation pathways from a T * /DP to b T to a T (top right) and from b T * / DP to a P to b P (bottom right). A gap region is indicated by two red lines on the former path (top right). The cartoon schematics illustrating the two pathways is shown on the left. To see this figure in color, go online. either resist the third ATP binding or likely convert to T-E-T* (rather than T-T*-E) if the third ATP binding succeeds by chance.
The TEN simulation induces the asymmetric neighbor-site opening upon ATP binding, as the atomistic TMD does Note that ATP binding and hydrolysis, along with the induced mechanical responses, involve substantial conformational changes with a characteristic time of up to microto milliseconds, which may not be easily sampled by equilibrium atomistic MD. To check whether the accelerated TMD and ensuing responses at the sub-microsecond timescale bear artifacts or capture the essential motions from the original slow dynamics, we also conducted CG simulations of the F 1 ring. We employed the single-beadper-residue elastic network (EN) description (56), which has been widely used to describe the slow or micro-to millisecond functional domain motions of protein (57)(58)(59). To make an easy comparison, we implemented targeted dynamic schemes in the EN model as well and then monitored closely the neighbor site-responses (see Supporting Material) (53)(54)(55). In particular, the forced E/T transition starting from the E-DP-T ring, and that starting from the E-E-E ring, were conducted at the CG level. Upon the E-DP-T to T-DP-T* transition, the C-terminal b-protrusion of the DP-site increased, indicating an opening, whereas the T-site did not show such an opening (see Fig. 2 D and Fig. S19). Upon the E-E-E to E-T-E transition, the asymmetric responses revealed were similar to those triggered by the TMD simulation, in which the downstream site showed opening, whereas the upstream site did not (see Fig. S20). Hence, regarding the conformational responses due to the inter-subunit coupling on the F 1 ring, agreement between the CG model and the atomistic-level description is obtained. The agreement indicates that the responses under the fast enforcement in the TMD simula-tions persist when enforcement takes place slowly in the TEN. It also suggests that the conformational responses upon ATP binding or hydrolysis may not be very slow or rate limiting. Instead, it may be the wait for ATP binding or hydrolysis that lasts long enough to be essentially rate limiting in the overall cycle.

DISCUSSION
To reveal kinetics essentials and structural dynamics mechanisms supporting high coordination of a prototypical ring-shaped NTPase, we investigated computationally the inter-subunit couplings that lead to intrinsic sequential performances of the F 1 -ATPase ring in the absence of the central g rotor. We first explored which types of inter-subunit couplings are kinetically feasible to allow sequential hydrolysis of the three active sites on the F 1 -ring through the stochastic Monte Carlo simulations. We imposed the primary couplings of the three independent ATP hydrolysis cycles by essentially enhancing the ADP and Pi release rates in one site (i.e., above the uni-site reaction rates) upon a certain neighborsite ATP binding or hydrolysis event in another site. We found that to support sequential hydrolysis in MF 1 , the ADP release needs to be accelerated >$10 5 -fold upon upstream-site ATP binding to the E-DP-T ring, and similarly for the ensuing Pi release from the same site; in BF 1 , on the other hand, the ADP release needs to be accelerated for above $10 3 fold, while the Pi release can be accelerated either along with the ADP release and/or upon downstream-site ATP hydrolysis in the T-P-T* ring. To elucidate the physical basis of these kinetically feasible couplings with structural detail, we next performed atomistic TMD simulations to enforce the conformational transition of the ATP binding or hydrolysis to one of the three chemical sites, and we monitored the following mechanical responses from the two neighbor sites. We found essentially the features below from the combined stochastic kinetic and structural dynamics simulations. The primary inter-subunit coupling that supports sequential hydrolysis with a directional bias is the ATP-binding-facilitated downstream-site product release, arising from the asymmetrical site opening inherent to the architecture of the trimerof-heterodimer ring Consistently, we found in the atomistic simulation of the E-DP-T ring that the downstream DP-site opens in response to the enforced E-site closing that mimics ATP binding. The site opening was partially characterized by a slight increase of the b-protrusion, the hinge bending angle, and the pocket size of the binding. Further examinations show notable conformational changes along with weakening of the hydrogen-bond network in the peripheral region of the DP-site. All these allosteric impacts induced by the E-site closing would likely facilitate ADP release from the DPsite. When the central g-rotor was included in the TMD simulation, the b DP -protrusion increase was notably enhanced. Close examination of the cross-correlation of the E-DP-T ring in the absence of the g rotor shows that the ATP-binding-induced conformational changes propagate asymmetrically from the E-site to the DP-and T-sites via the a E -b DP and b E -a T -b T paths, respectively. The asymmetrical downstream site opening is also preserved upon the induced site closing that mimics the first ATP binding to the empty E-E-E ring. The asymmetrical responses thus appear to be inherent to the architecture of the trimer-of-the-heterodimer (a-b) ring, in particular, as aand b-subunits differ and alternate around the ring, whereas the chemical active site largely locates on b. The inclusion of the g-rotor into the center of the ring is able to enhance the asymmetrical responses significantly, which either promotes ADP release (and the initial Pi release) or biases the second ATP binding to the downstream site. In particular, the bias for the second ATP binding downstream allows the sequential hydrolysis to proceed directionally (counterclockwise viewed from the C-terminal side).
Sequential hydrolysis is also supported by proper timing and acceleration of Pi release, which follows ADP release either quickly upon upstream-site ATP binding or later upon downstream-site ATP hydrolysis; Pi release is completed in charge hopping in the simulation On the other hand, Pi release can be facilitated via two different mechanisms (see Fig. 1 C), either upstream-site ATP binding that induces ADP release first (MF 1 (18)) or downstream T*-site ATP hydrolysis (BF 1 (19)). Direct support for the first mechanism comes from the bovine heart MF 1 structure per se (T-P-T*; PDB: 1W0J) (51), in which the Pi group in the P-site (after ADP release) is located nearby the P-loop, a marginally stabilized state, rather than in the innermost tightly bound state (37). That is, ATP binding to the ring (from E-DP-T to T-DP-T*) not only destabilized ADP from the DP-site, but also destabilized the bound Pi, so that Pi moved from the tightly bound state to the marginally stabilized state. The release of Pi thereafter then becomes comparatively easy.
Nevertheless, our equilibrium MD simulation of the T-P-T* ring was not yet able to capture the Pi release from the P-site within hundreds of nanoseconds. In the equilibrium simulation, the Pi group was associated with the b P-loop as well as the arginine finger aArg373. The other arginine finger, aArg143, was trapped initially by association with aAsp314 in the P-site. Nicely, in contrast, a complete Pi-release event was revealed in the TMD simulation, as the P-site mechanistically responded to the enforced hydrolysis in the T*-site. The P-loop retracted and Arg143 was able to switch occasionally toward Arg373, whereas the three negatively charged residues from b P also repelled Pi to assist the release. Consequently, the chance that Pi is caught by Arg143 and dissociates from the P-loop increases significantly, and P-loop dissociation becomes critical for further charge hopping, and the final release of Pi.
Compared with the significant open-to-closed conformational changes in the ATP binding site, ATP-hydrolysisinduced conformational changes are rather subtle. We found that the inactive site at the b T *-a P interface, along with a b-sheet region on a P , actually bridged the mechanistic pathway to propagate the subtle conformational changes from the T*-site to the P-site, whereas the other way of propagation was broken through the inactive site at the a T *-b T interface. In brief, ATP hydrolysis does not generate substantial responses on the protein ring; rather, it triggers local directional conformational propagation via the inactive site and a restricted structural element. Besides, in the T-P-T* ring, the P-site upstream of the T*-site is more open and likely much more flexible than the downstream T-site; hence, it appears easier for the mechanical responses to propagate upstream than downstream.
We also found additional couplings or constraints that would help the sequential hydrolysis. An explicit constraint to prevent the third ATP binding to the MF 1 ring (or inhibit the 3-T population) would improve the sequential performance, since the 2-T (T-E-T*) configuration is on the dominant reaction path of MF 1 . The 2-T configuration can easily turn into 3-T without the constraint, thus interfering with the sequential scheme. The TMD simulation enforcing a third ATP binding to the E-T*-T ring consistently demonstrated significant destabilization of the neighboring sites. On the other hand, the BF 1 ring achieves sequential performance without the explicit constraint to exclude 3-T, as such a 2-T configuration is not on the dominant reaction path. In addition, we effectively enhanced the ATP hydrolysis rate in the T*-site, when a second ATP binds to the ring to form a T-site. The rate enhancement in the hydrolysis-ready intermediate T*-site ensures that hydrolysis takes place sufficiently fast and the site that binds ATP early can hydrolyze early most of the time. Anyhow, these constraints or couplings were not very stringently imposed, and there was a significant chance that the reactions went off-path to configurations such as 3-T or 2-DP, which might also account for some non-optimal mechanochemical couplings detected early (60).
Tight coupling is expected between ATP binding and ADP release, and the strength of the coupling can be substantially enhanced by the central g-rotor; the coupling between ATP hydrolysis and Pi release is notable even in the absence of the g-rotor The rotary sequential hydrolysis of F 1 -ring is basically supported by chemical free energy through the three ATP cycles, which are coordinated with certain phase differences. The coordination also demands free-energy input and dissipation (61). The kinetic rate enhancements in the inter-subunit couplings require lowering activation barriers of the facilitated transitions, e.g., for the hydrolysis product (ADP or Pi) release. For such couplings, either the product binding affinity (or the dissociation constant) is maintained, or the product-rebinding rate remains constant, which requires free-energy compensation from the neighboring unit. For example, to enhance the ADP release rate $10 5fold (in MF 1 ), it requires up to $12 k B T to destabilize the DP-site (with a constant ADP-rebinding rate), and the energy compensation should come from the neighbor-site ATP binding (e.g., by also destabilizing the ATP binding to the T-site). Since the chemical free energy is mostly dissipated through the rotational degree of freedom in the presence of the g-rotor (62,63), one expects that the g-rotor would play a significant role in strongly coupling the ATP binding to the next-site ADP release, both structurally and energetically. Current studies indeed show that the b DP -protrusion responds more significantly to the enforced ATP binding in the presence of the g-rotor than in its absence.
In comparison, the ATP-hydrolysis-facilitated Pi release (rate enhancement $10 3 -fold) appears to require less energetic compensation in the coupling if there is any, so we could actually capture the Pi release event in the absence of the g-rotor. As such, we infer that the central g-rotor dictates the inter-subunit coupling more significantly in the ATP binding step than in the ATP hydrolysis step, which leads to stronger inter-subunit couplings or higher coordination in the original F 1 -ATPase with the rotor than in the stator ring only. As a matter of fact, considering the recent MD studies on the g-shaft rotation and the Pi release (37), together with our current simulation results, we suggest that the initial stage of the Pi release can also be facilitated by the g-shaft rotation that accompanies the ATP binding and the ADP release. Complete Pi release can be further promoted by the neighbor-site ATP hydrolysis in the bacterial F 1 , which can couple with the additional g-shaft rotation.
According to our study, one can further tune the inter-subunit coupling kinetics to allow a significant increase in the overall cycling rate of F 1 , approaching experimentally measured values for the full F 1 system with the rotor (see Tables S3 and S4). Hence, one can see that the rotor effectively plays a role in strengthening and further modulating the inter-subunit couplings on the ring, and consequently in promoting the overall hydrolysis rate. Based on current work, it would be promising to determine how exactly the central g-rotor contributes to the F 1 inter-subunit coordination for the respective steps of ATP binding and hydrolysis. Indeed, the ATP binding and hydrolysis transitions, along with their coordination in the ring assembly, have only been phenomenologically modeled in current work, and they deserve more substantial investigation in future work.

CONCLUSIONS
Combining stochastic simulations of tri-site chemical kinetics of the F 1 stator ring with targeted atomistic MD and coarse-grained EN simulations, we inferred the most crucial inter-subunit couplings leading to sequential hydrolysis on the F 1 ring: ATP binding facilitates ADP release from a downstream DP-site, along with Pi release from the same site, whereas complete Pi release can be further facilitated by ATP hydrolysis downstream. The couplings come from asymmetrical neighbor-site opening/loosening upon current site closing/tightening produced by the ATP binding/hydrolysis. The dominant conformational asymmetry, demonstrated upon ATP binding, appears to be embedded in the trimer-of-heterodimer ring, owing largely to the alternating arrangement of aand b-subunits. Additionally, a minor structural dynamics asymmetry is revealed upon subtle conformational transition under ATP hydrolysis, which impacts the neighbor sites differently via subtle structural variations. The mechanistic propagation around the ring is therefore modulated also by the ligand (ATP, ADP, or Pi) bound status in the neighboring sites. Furthermore, preventing a third ATP from binding to the assembled ring, as well as allowing a hydrolysis-ready intermediate in the ring to have an elevated hydrolysis rate, also supports the sequential hydrolysis on the F 1 ring. Though the overall cycling rate in our simulation of the bacterial F 1 ring matches with the experimental detection of the rotor-less system, it should be noted that the full F 1 in the presence of the rotor rotates and cycles much faster, revealing a central role played by the rotor in enhancing inter-subunit coupling on the ring. The large discrepancy between the cycling rates of mitochondrial and bacterial species of F 1 in the rotorless case does not necessarily show in the presence of the rotor, indicating further inter-subunit modulation from the rotor. It would be highly interesting to pursue whether comparable coupling scenarios apply to evolutionarily connected ring-shaped protein enzymes working on a central substrate of protein or nucleic acid.

AUTHOR CONTRIBUTIONS
J.Y. designed the research. L.D. and H.F. performed the research. L.D. and H.F. analyzed the data. J.Y., H.F., and L.D. wrote the article.


extfieldsofstudy: Chemistry Medicine

text:
Effect of the Elemental Composition of Precursors from Amino Acids and Their Binary Mixtures on the Photoluminescent Intensity of Carbon Nanodots

We report on the photoluminescent (PL) properties of carbon nanodots (CNDs) doped with nitrogen and sulfur obtained by the pyrolytic carbonization of amino acids as precursors. Prepared CNDs exhibit stable PL emission under a wide variety of aqueous conditions. The results also provided the way to tune a PL intensity of CNDs by varying the amount of heteroatoms in precursors with a binary mixture of amino acids. The PL quantum yields of the obtained CNDs were determined to be from 0.079 to 0.571.

Introduction
Recently, photoluminescent nanocarbons, including carbon nanotubes, detonation diamonds 1 and graphene quantum dots (GQDs), 2 have received intensive attention concerning applications to analytical and biochemical research. 3 As an alternative to organic fluorophores 4 and toxic semiconductor quantum dots, 5 luminescent nanocarbons are superior in terms of chemical inertness, environmental suitability and stable photoluminescence (PL). Among them, carbon nanodots (CNDs), which are generally obtained by relatively mild synthetic conditions and simple procedures, possess practical dispersibility in water owing to oxygenated functional groups on the surface. Utilizing the affinity between functional groups on the CNDs surface and analyte molecules or ions, CNDsbased PL sensing systems were reported for pH, 6,7 ions 8,9 and biological substances. 10,11 In general, above-mentioned systems mainly depend on the change in the PL intensity of CNDs upon interaction with the target analyte. On the basis of photochemical processes, conventional response mechanisms, including electrochemiluminescence, 12 fluorescence resonance energy transfer 13,14 and inner filter effect, 15 are also employed for CNDbased sensing systems. Regardless of the response mechanisms, the PL intensity of CNDs is an influencing factor for improving the efficiencies and sensitivities of luminescence-based detection and determination. Therefore, it is highly desired to prepare CNDs with high PL intensity, i.e., PL quantum yield (QY), for developing effective sensing systems.
The PL properties of CNDs have been investigated since luminescent CNDs were first discovered during the purification of carbon nanotubes. 16 CNDs have been mainly prepared by oxidative procedures for the treatment of various carbon sources, such as graphite, 17 candle soot, 18 and organic compounds. 19 Several synthetic approaches 20 were applied to tune the PL properties of CNDs by a post-treatment, such as chemical reduction, 21 organosilane-functionalization, 22 and electrochemical agitation. 23 Among them, hydrothermal 24 and microwaveassisted 25 treatments of organic precursors, natural products 26 and raw materials 27 have been widely used to prepare CNDs. Although CNDs have become attractive as PL probes, the QY values of as-prepared CNDs are not very high (often less than 0.2; see Table S1, Supporting Information) in many cases. To overcome these difficulties, heteroatom-doping has been actively investigated, since it is considered to be the most promising candidate to dope nitrogen and sulfur into CNDs, resulting in improvements of the QY values. 28,29 In this report, we focus on the effect of the elemental composition of nitrogen and sulfur in precursors on the PL properties and QY values of obtained CNDs. We used several amino acids as precursors for the preparation of CNDs doped with nitrogen and sulfur. Since the elemental composition of these amino acids are clearly defined, we expect that they and their mixtures our suitable precursors for preparing CNDs with a series of different doping levels of hetero atoms. Pyrolytic carbonization in an electronic furnace was employed as a low-cost and efficient method for the preparation of CNDs. Three kinds of amino acids-glycine, cysteine and glutamic acid-were used for precursors in this study. The PL properties of obtained CNDs were first confirmed regarding the linear relationship between the absorbance at the excitation maximum and the PL intensity at the emission maximum; then, QY values were determined. The PL emission stabilities of obtained CNDs were also examined concerning the effect of the pH, ionic strength and excitation wavelength in aqueous solutions.

Pyrolytic synthesis of CNDs
The general procedure for the synthesis of CND was conducted as follows. Briefly, the precursor was dissolved in water and heated in an electric furnace at 250 C for 2 h. After heating, the crude product was cooled to room temperature and then dispersed in water. Suction filtration and centrifugal filtration were applied to the solution, and CND stock solutions were obtained. Hereafter, CNDs obtained from glycine, cysteine and glutamic acid were abbreviated as G-CND, C-CND and E-CND, respectively.

Spectral measurements of CNDs
Sample solutions for spectral measurements were prepared by diluting stock solutions of CNDs with water or appropriate buffer solutions.
The concentrations of CNDs in the measurement samples were defined by the absorbance at the excitation maximum (Axxx, xxx denotes the excitation wavelength, which depends on the type of CNDs). Unless otherwise stated, Axxx were less than 0.05 for PL spectra measurements. The quantum yield of the CNDs were determined using quinine sulfate (Φ = 0.546 in 0.5 M H2SO4) 30 as a standard. The effect of the sample conditions on the PL intensity were examined for pH values of from 2 to 11 or ionic strength up to cNaCl = 4.5 mol dm -3 .

PL properties of CNDs from amino acids
The UV-vis absorption spectra of G-CND dispersed in water (Fig. 1, dotted lines) show absorption peaks (λabs) centered at 306 nm, which may be attributed to the n-π* transition of the C=O double bond. G-CNDs, also have emission (solid lines, λem) spectra, with symmetrical and featureless peaks, recognized at 390 nm. The linearity ranges between the absorbance at the excitation maximum and the PL intensity of the emission maximum is depicted in Fig. 1 inset. Under the optimum conditions, the PL intensity of CNDs (Supporting Information, Fig. S1 for C-CND, Fig. S2 for E-CND) exhibited linear relationships with the absorbance at the excitation maximum of at least A = 0.05.
Like most CNDs reported, the emission wavelength of the CNDs depends on the excitation wavelength, as shown in Fig. 2. Namely, with the increase of the excitation wavelength, the maximum emission band is shifted to longer wavelength and the peak intensity decreases. This kind of excitation-dependent PL behavior was frequently reported in the literature, 7 and ascribed to the distribution of different emissive trap sites and the difference in the particle size of the CNDs.
The PL intensity of CNDs is strong and stable in a neutral pH range (Fig. S3) and in a wide range of ionic strengths (Fig. S4). In the acidic and basic pH region, both the excitation and emission intensity were altered, whereas the absorbance at the excitation wavelength remained essentially unchanged. The effect of the pH values can be presumptively understood in terms of the change in the surface charge owing to the protonation-deprotonation of surface functional groups. 31 Table 1 summarizes the elemental composition of precursor amino acids and the PL properties of obtained CNDs. Concerning the precursors, the absorption and PL wavelength of the CNDs were hardly affected; by contrast, the QY values were drastically varied. Heteroatom-doping on the CNDs has been actively pursued since they are considered to improve QY, owing to the synergistic effect of nitrogen-sulfur co-doping. Contrary to an expectation based on the effect of heteroatomdoping, C-CND with the highest N,S-content studied here showed the lowest QY value. The results described above indicate that the improvement in QY is not directly proportional on the N,S-content of the precursors.

QY values of CNDs from binary mixtures of amino acids
We further examined the relationship between the elemental composition of the precursors and the QY values of the obtained CNDs. It was found that E-CND showed the highest QY with the lowest heteroatom content in previous experiments. The results for the three types of CNDs enabled us to assume following hypotheses; (i) Nitrogen doping of the lower content in the precursor (i.e., E-CND) effectively improves the QY values of the CNDs. (ii) Nitrogen doping of the higher content in the precursor (i.e., G-CND) provides an inverse effect on the QY improvement.
(iii) Some degree of nitrogen-sulfur co-doping (i.e., C-CND) may result in a negative synergistic effect. To explore a further improvement in the QY values of CNDs, glycine-glutamic acid (abbreviated as G1-x-Ex system) and cysteine-glutamic acid (C1-x-Ex system) binary mixtures with a series of molar fractions of glutamic acid (0 < x < 1) were used to synthesize CNDs. Figure 3 shows the QY values of the obtained CNDs and the molar fraction of glutamic acid in G1-x-Ex and C1-x-Ex systems. Increasing the molar fraction of glutamic acid up to approximately x = 0.5 resulted in an increase in the QY values of the G1-x-Ex system, but no further increase was observed up to x = 1.0, converging with the QY value of E-CND. As summarized in Tables S2 and S3, the molar fraction of glutamic acid increases, while the N-content of the G1-x-Ex system decreases.
This dependency suggested that the enhancement in QY of nitrogen doping does not correlate to the amount of nitrogen; also ca. 10% of N-content is optimum for the G1-x-Ex system. A similar increase in the QY values was also observed for the C1-x-Ex system until x = 0.6, resulting in the QY value being at a maximum of 0.571, which exceeds that of E-CND. As a result, the maximum QY values in the C1-x-Ex system were found for both the N-and S-contents to be ca. 10% in the elemental composition of the precursors.
Although the PL mechanisms and electronic properties of CNDs are not fully understood, it is frequently proposed that the PL of the CNDs can be attributed to the radiative recombination of electrons and holes trapped on the CDs surface. 32 According to the literature, Dong et al. assumed an enhancement in the QY values of N,S-doped CNDs in two aspects. 31 First, the doping of nitrogen to CNDs introduces new types of surface states, which are able to facilitate radiative recombinations, resulting in increases in the QY values. Second, the co-existence of sulfur together with nitrogen further enhances the effect of nitrogen atoms in doped CND through a cooperative effect. As shown in Fig. 3, the cooperative effect on QY is recognized for the C1-x-Ex system over the G1-x-Ex system.

Conclusions
In summary, nitrogen and sulfur co-doped CNDs have been prepared by the pyrolytic carbonization of amino acids and their binary mixtures as precursors. The obtained CNDs show stable and excitation-dependent PL emission with tunable PL QY depending on the elemental composition of precursors. Even though the exact mechanism and relationships are still unclear, it is reasonable to believe that the doping of nitrogen and sulfur can improve the QY values of CNDs, whose optimum content were revealed to be ca. 10% in precursors for the systems studied here. Further work on the extending synthetic scale and the direct elemental analysis of the prepared-CNDs in the present system is in progress in our laboratory to clarify the relationship between the elemental composition of the precursors and that of the resultant CNDs.