Combined Classical Molecular Dynamics Research Articles

Zn/Ce-layered double hydroxide for adsorptive removal of doxycycline from water

Since antibiotic overuse created various environmental issues, antibiotic management and separation are critical in ecological research. In this regard, the main objective of this work was to design a simple and reliable solvothermal-synthesis-based sorbent for removing antibiotics such as doxycycline (DOX). The used sorbent was Zn/Ce-layered double hydroxide (Zn/Ce-LDH), and its layered structure was confirmed by the X-ray diffraction (XRD), field emission scanning electron microscopy (SEM), transmission electron microscopy (TEM) analysis. In addition, the Brunauer-Emmett-Teller (BET) test showed the specific surface area of the Zn/Ce-LDH achieved 45.17 m2 g−1. The sorbent was shown to have a high capability to remove DOX (the maximum experimental adsorption capacity of 1297 mg g−1) at the low equilibrium contact time of 15 min. Also, the obtained negative value of Gibbs free energy (ΔG°), the enthalpy (ΔH°), and the entropy (ΔS°) at the investigated temperatures reveal the fact that the involved adsorption process had spontaneous and exothermic features. Besides, the pseudo-second-order kinetic model favourably described DOX adsorption on the Zn/Ce LDH surface. Furthermore, a combination of classical molecular dynamics and Monte Carlo simulations were utilized to investigate the adsorption properties of DOX on the (001) and (010) Zn/Ce-LDH surfaces. The theoretical findings supported the possibility of DOX coordination with Zn/Ce atoms.

Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems.

Molecules that can undergo reversible chemical transformations following the absorption of light, the so-called molecular photoswitches, have attracted increasing attention in technologies, such as solar energy storage. Here, the optical and thermochemical properties of the photoswitch are central to its applicability, and these properties are influenced significantly by solvation. We investigate the effects of solvation on two norbornadiene/quadricyclane photoswitches. Emphasis is put on the energy difference between the two isomers and the optical absorption as these are central to the application of the systems in solar energy storage. Using a combined classical molecular dynamics and quantum mechanical/molecular mechanical computational scheme, we showcase that the dynamic effects of solvation are important. In particular, it is found that standard implicit solvation models generally underestimate the energy difference between the two isomers and overestimate the strength of the absorption, while the explicit solvation spectra are also less red-shifted than those obtained using implicit solvation models. We also find that the absorption spectra of the two systems are strongly correlated with specific dihedral angles. Altogether, this highlights the importance of including the dynamic effects of solvation.

Hydration structure and dynamics, ultraviolet–visible and fluorescence spectra of caffeine in ambient liquid water. A combined classical molecular dynamics and quantum chemical study

The hydration structure and related dynamics of caffeine diluted in ambient liquid water have been extensively studied by performing classical molecular dynamics simulations, using our previously developed potential model of caffeine and the TIP4P/2005 water model. The results obtained have revealed that the first hydration shell of caffeine contains on average 56 water molecules. Hydrated caffeine forms in total 3 hydrogen bonds with its neighbor water molecules, with the Ocaffeine … Hwater hydrogen bonds exhibiting similar lifetimes with the ones corresponding to Owater … Hwater hydrogen bonds in liquid water. The self-diffusion coefficient of caffeine has been found to be four times lower than the corresponding value for water, being also in agreement with recent experimental measurements. The presence of water molecules inside the solvation shell of caffeine changes significantly their low-frequency intermolecular vibrations, as reflected on the calculated atomic velocity time correlation functions and corresponding spectral densities. Using the estimated average intermolecular structure of the first hydration shell of caffeine, the molecular cluster caffeine@W56 was optimized via quantum chemical calculations and subsequently the time-dependent density functional theory was used in order to predict the ultraviolet–visible and fluorescence spectra of hydrated caffeine. The results obtained are in agreement with recent experimental studies, which have proposed that such spectroscopic measurements can be used for the direct determination of alkaloids in aqueous extracts of natural products. In this framework, multi-scale molecular modelling providing accurate predictions of experimental data could also be a very useful tool, linking theoretical physical chemistry with analytical chemistry applications.

Impact of Structure, Coupling Scheme, and State of Interest on the Energy Transfer in CP29.

The Qy and Bx excitation energy transfer (EET) in the minor light-harvesting complex CP29 (LHCII B4.1) antenna complex of Pisum sativum was characterized using a computational approach. We applied Förster resonance energy transfer (FRET) and the transition density cube (TDC) method to estimate the Coulombic coupling, based on a combination of classical molecular dynamics and quantum mechanics/molecular mechanics calculations. Employing TDC instead of FRET mostly affects the EET between chlorophylls (Chls) and carotenoids (Crts), as expected due to the Crts being spatially more challenging for FRET. Only between Chls, effects are found to be small (about only 0.1 EET efficiency change when introducing TDC instead of FRET). Effects of structural sampling were found to be small, illustrated by a small average standard deviation for the Qy state coupling elements (FRET/TDC: 0.97/0.94 cm-1). Due to the higher flexibility of the Bx state, the corresponding deviations are larger (FRET/TDC between Chl-Chl pairs: 17.58/22.67 cm-1, between Crt-Chl pairs: 62.58/31.63 cm-1). In summary, it was found for the Q band that the coupling between Chls varies only slightly depending on FRET or TDC, resulting in a minute effect on EET acceptor preference. In contrast, the coupling in the B band spectral region is found to be more affected. Here, the S2 (1Bu) states of the spatially challenging Crts may act as acceptors in addition to the B states of the Chls. Depending on FRET or TDC, several Chls show different Chl-to-Crt couplings. Interestingly, the EET between Chls or Crts in the B band is found to often outcompete the corresponding decay processes. The individual efficiencies for B band EET to Crts vary however strongly with the chosen coupling scheme (e.g., up to 0.29/0.99 FRET/TDC efficiency for the Chl a604/neoxanthin pair). Thus, the choice of the coupling scheme must involve a consideration of the state of interest.

Electrons Surf Phason Waves in Moiré Bilayers.

We investigate the effect of thermal fluctuations on the atomic and electronic structure of a twisted MoSe2/WSe2 heterobilayer using a combination of classical molecular dynamics and ab initio density functional theory calculations. Our calculations reveal that thermally excited phason modes give rise to an almost rigid motion of the moiré lattice. Electrons and holes in low-energy states are localized in specific stacking regions of the moiré unit cell and follow the thermal motion of these regions. In other words, charge carriers surf phason waves that are excited at finite temperatures. We also show that such surfing survives in the presence of a substrate and frozen potential. This effect has potential implications for the design of charge and exciton transport devices based on moiré materials.

Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.

A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM)and alchemical free energy (AFE) simulations to elucidate the atomic-levelsolution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol-1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity-pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.

Disulfide bond reduction and exchange in C4 domain of von Willebrand factor undermines platelet binding

BackgroundThe von Willebrand factor (VWF) is a key player in regulating hemostasis through adhesion of platelets to sites of vascular injury. It is a large, multi-domain, mechano-sensitive protein that is stabilized by a net of disulfide bridges. Binding to platelet integrin is achieved by the VWF-C4 domain, which exhibits a fixed fold, even under conditions of severe mechanical stress, but only if critical internal disulfide bonds are closed. ObjectiveTo determine the oxidation state of disulfide bridges in the C4 domain of VWF and implications for VWF’s platelet binding function. MethodsWe combined classical molecular dynamics and quantum mechanical simulations, mass spectrometry, site-directed mutagenesis, and platelet binding assays. ResultsWe show that 2 disulfide bonds in the VWF-C4 domain, namely the 2 major force-bearing ones, are partially reduced in human blood. Reduction leads to pronounced conformational changes within C4 that considerably affect the accessibility of the integrin-binding motif, and thereby impair integrin-mediated platelet binding. We also reveal that reduced species in the C4 domain undergo specific thiol/disulfide exchanges with the remaining disulfide bridges, in a process in which mechanical force may increase the proximity of specific reactant cysteines, further trapping C4 in a state of low integrin-binding propensity. We identify a multitude of redox states in all 6 VWF-C domains, suggesting disulfide bond reduction and swapping to be a general theme. ConclusionsOur data suggests a mechanism in which disulfide bonds dynamically swap cysteine partners and control the interaction of VWF with integrin and potentially other partners, thereby critically influencing its hemostatic function.

A Crystalline Dimeric Steroidal Diboronate with Electronically Impeded Rotation

The dimeric steroid SMR-3, featuring a 1,4-phenyldiboronic ester flanked by two pregnan-triol frameworks, was synthesized to explore the intramolecular dynamics of its central component. The structural data from single-crystal X-ray diffraction studies and the Hirshfeld analyses indicate small steric effects around the aromatic ring that should favor the intended motion. However, solid-state NMR data obtained through VT 13C{1H} CPMAS and 2H spin-echo experiments, using the deuterated analogue SMR-3D4, revealed that this component is rigid even at temperatures where other reported steroidal molecular rotors experience fast rotation (85 °C). A combination of classical molecular dynamics, molecular mechanics, and correlated ab initio calculations allowed us to distinguish the steric and electronic factors that restrict the potential motion in this compound. The experimental and computational data reveal that electronic components dominate the behavior and are responsible for the high rotational barrier in the SMR-3 crystal.

Recognizing the Binding Pattern and Dissociation Pathways of the p300 Taz2-p53 TAD2 Complex.

The dynamic association and dissociation between proteins are the basis of cellular signal transduction. This process becomes much more complicated if one or both interaction partners are intrinsically disordered because intrinsically disordered proteins can undergo disorder-to-order transitions upon binding to their partners. p53, a transcription factor with disordered regions, plays significant roles in many cellular signaling pathways. It is critical to understand the binding/unbinding mechanism involving these disordered regions of p53 at the residue level to reveal how p53 performs its biological functions. Here, we studied the dissociation process of the intrinsically disordered N-terminal transactivation domain 2 (TAD2) of p53 and the transcriptional adaptor zinc-binding 2 (Taz2) domain of transcriptional coactivator p300 using a combination of classical molecular dynamics, steered molecular dynamics, self-organizing maps, and time-resolved force distribution analysis (TRFDA). We observed two different dissociation pathways with different probabilities. One dissociation pathway starts from the TAD2 N-terminus and propagates to the α-helix and finally the C-terminus. The other dissociation pathway is in the opposite order. Subsequent TRFDA results reveal that key residues in TAD2 play critical roles. Besides the residues in agreement with previous experimental results, we also highlighted some other residues that play important roles in the disassociation process. In the dissociation process, non-native interactions were formed to partially compensate for the energy loss due to the breaking of surrounding native interactions. Moreover, our statistical analysis results of other experimentally determined complex structures involving either Taz2 or TAD2 suggest that the binding of the Taz2-TAD2 complex is mainly governed by the binding site of Taz2, which includes three main binding regions. Therefore, the complexes involving Taz2 may follow similar binding/unbinding behaviors, which could be studied together to generate common principles.

Influence of the Greater Protein Environment on the Electrostatic Potential in Metalloenzyme Active Sites: The Case of Formate Dehydrogenase.

The Mo/W-containing metalloenzyme formate dehydrogenase (FDH) is an efficient and selective natural catalyst that reversibly converts CO2 to formate under ambient conditions. In this study, we investigate the impact of the greater protein environment on the electrostatic potential (ESP) of the active site. To model the enzyme environment, we used a combination of classical molecular dynamics and multiscale quantum-mechanical (QM)/molecular-mechanical (MM) simulations. We leverage charge shift analysis to systematically construct QM regions and analyze the electronic environment of the active site by evaluating the degree of charge transfer between the core active site and the protein environment. The contribution of the terminal chalcogen ligand to the ESP of the metal center is substantial and dependent on the chalcogen identity, with similar, less negative ESPs for Se and S terminal chalcogens in comparison to O regardless of whether the metal is Mo or W. The orientation of the side chains and conformations of the cofactor also affect the ESP, highlighting the importance of sampling dynamic fluctuations in the protein. Overall, our observations suggest that the terminal chalcogen ligand identity plays an important role in the enzymatic activity of FDH, suggesting opportunities for a rational bioinspired catalyst design.

Wigner energy in irradiated graphite: A first-principles study

First-principles calculations were performed to examine the defect-induced energy storage in graphite. The accumulation of energy resulting from inducing defects in graphite is a well-known phenomenon. Given the recent interest in exploiting this process for energy-storing purposes, more careful investigation is necessary. Some of the earliest studies of damaged graphite, and the stored energy associated with that, were motivated by the associated technological issues in nuclear reactor operation. A large number of excited state defects, for example Frenkel pairs, can be generated in graphite through bombardment of high-energy neutrons. The sudden release of this energy (also called Wigner energy) poses a serious concern to the safe operation of nuclear reactors. At the same time, controlled defect generation in graphite using neutron/ion irradiation might represent a potential energy storage mechanism. In recently published papers, the design of an integrated energy system that couples a nuclear reactor with a Wigner effect-based energy storing system was proposed. To accurately estimate the performance that can be achieved in terms of stored energy density through defect generation, density functional theory (DFT) based first-principles calculations were performed. In this work, stored energy accumulation was modeled in two ways - by Frenkel pair accumulation and overlapping collision cascade methods. The former was done with ab initio molecular dynamics (AIMD) simulations, and the latter was done with combined classical molecular dynamics (MD) and AIMD simulations. The agreement between the calculated and experimental results for how stored energy changes with dosage suggests that this model could be useful for the on-going research into damaged graphite as an energy storage medium.

Effect of interfacial structures on phonon transport across atomically precise Si/Al heterojunctions

Phonons are important carriers of energy and information in many cryogenic devices used for quantum information science and in fundamental physics experiments such as dark matter detectors. In these systems phonon behaviors can be dominated by interfaces and their atomic structures; hence, there is increasing demand for a more detailed understanding of interfacial phonon transport in relevant material systems. Previous studies have focused on understanding thermal transport over the entire phonon spectrum at and above room temperature. At ultralow temperatures, however, knowledge is missing regarding athermal phonon behavior due to the challenge in modeling the extreme conditions in microscale, heterogeneous cryogenic systems, as well as extracting single-phonon information from a large ensemble. In this paper, we delineate the effects of interfacial atomic structures on phonon transport using a combination of classical molecular dynamics (MD) and phonon wave-packet simulations, to illustrate the consistency and differences between the ensemble- and single-phonon dynamics. We consider three single-crystal Si surface reconstructions---$(1\ifmmode\times\else\texttimes\fi{}1), (\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ and $(7\ifmmode\times\else\texttimes\fi{}7)$---and model both experimentally observed $\mathrm{Si}(1\ifmmode\times\else\texttimes\fi{}1)/\mathrm{Al}$ interfaces and hypothesized $\mathrm{Si}(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$/Al and $\mathrm{Si}(7\ifmmode\times\else\texttimes\fi{}7)/\mathrm{Al}$ interfaces. The overall interfacial thermal conductance calculated from non-equilibrium MD shows that for the $\mathrm{Si}(1\ifmmode\times\else\texttimes\fi{}1)/\mathrm{Al}$ system, the presence of Al twin boundaries can hinder phonon transport and reduce thermal conductance by 2--12% relative to single-crystal Al; whereas the Si $(\sqrt{3}\ifmmode\times\else\texttimes\fi{}\sqrt{3})$ and $(7\ifmmode\times\else\texttimes\fi{}7)$ reconstructions can enhance it by 6--19%. Normal mode decomposition reveals that both the increase and decrease in conductance are related to inelastic phonon scattering. Single-phonon wave-packet simulations predict phonon transport properties consistent with non-equilibrium MD, while further suggesting that phonon polarization conversion is significant even when elastic transmission dominates, and that the interfacial structures have anisotropic impacts on atomic vibrations along different lattice directions. Our findings suggest avenues for achieving selective phonon transport via controlling interfacial structures of materials using atomically precise fabrication techniques, and that the phonon wave-packet formalism is a potentially powerful method for developing a detailed understanding of non-equilibrium phenomena in the low-temperature limit.

Ultrafast dynamics and scattering of protic ionic liquids induced by XFEL pulses.

X-rays are routinely used for structural studies through scattering, and femtosecond X-ray lasers can probe ultrafast dynamics. We aim to capture the femtosecond dynamics of liquid samples using simulations and deconstruct the interplay of ionization and atomic motion within the X-ray laser pulse. This deconstruction is resolution dependent, as ionization influences the low momentum transfers through changes in scattering form factors, while atomic motion has a greater effect at high momentum transfers through loss of coherence. Our methodology uses a combination of classical molecular dynamics and plasma simulation on a protic ionic liquid to quantify the contributions to the scattering signal and how these evolve with time during the X-ray laser pulse. Our method is relevant for studies of organic liquids, biomolecules in solution or any low-Z materials at liquid densities that quickly turn into a plasma while probed with X-rays.

Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation

A combination of classical molecular dynamics (MD) simulation and ab initio fragment molecular orbital (FMO) calculation was applied to a complex formed between the main protease of the new coronavirus and the inhibitor N3 to calculate interactions within the complex while incorporating structural fluctuations mimicking physiological conditions. Namely, a statistical evaluation of interaction energies between N3 and amino acid residues was performed by processing a thousand of structure samples. It was found that relative importance of each residue is altered by the structural fluctuation. The MD-FMO combination should be promising to simulate protein related systems in a more realistic way.

The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair.

The Watson–Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine–cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m−1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m−1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m−1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.

Mechanism for Rapid Conversion of Amines to Ammonium Salts at the Air-Particle Interface.

The effect of sulfuric acid (SA) concentrations on heterogeneous reactions of amines such as methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA) at the air-particle interface is investigated using combined classical molecular dynamics, Born-Oppenheimer molecular dynamics, and quantum chemical calculations. The results show that the mixtures of these amine vapors can accumulate at the air-particle interface and then participate in two types of heterogeneous reactions depending on the SA concentrations in the aqueous particles. At high SA concentrations, amines are neutralized by H3O+ and form ammonium salts within only a few picoseconds. At low SA concentrations, amines mainly proceed by hydrolysis reactions and produce ionic pairs of ammonium and OH-. However, the formed ionic pair is extremely unstable, and the reverse reaction takes place. Considering that the salt conversion time scales of amines at high SA concentrations are 2.5-15 times faster than those at low SA concentration, amine accumulation at high acidity particles is more favored.

Transport Properties of Ionic Liquid and Sodium Salt Mixtures for Sodium-Ion Battery Electrolytes from Molecular Dynamics Simulation with a Self-Consistent Atomic Charge Determination.

Ionic liquid (IL) has been considered as a potential electrolyte for developing next-generation sodium-ion batteries. A highly concentrated ionic system such as IL is characterized by the significant influence of intramolecular polarization and intermolecular charge transfer that vary with the combination of cations and anions in the system. In this work, a self-consistent atomic charge determination using the combination of classical molecular dynamics (MD) simulation and density functional theory (DFT) calculation is employed to investigate the transport properties of three mixtures of ILs with sodium salt relevant to the electrolyte for a sodium-ion battery: [1-ethyl-3-methylimidazolium, Na][bis(fluorosulfonyl)amide] ([C2C1im, Na][FSA]), [N-methyl-N-propylpyrrolidinium, Na][FSA] ([C3C1pyrr, Na][FSA]), and [K, Na][FSA]. The self-consistent method is versatile to address the intramolecular polarization and intermolecular charge transfer in response to the cation-anion combination, as well as the variation in their compositions. The structure and dynamic properties of IL mixtures obtained from the method are in line with those from the experimental works. The comparison to the Nernst-Einstein estimates shows that the electrical conductivity is reduced due to correlated motions among the ions, and the contribution to the conductivity from each ion species is not necessarily ranked in the same order as the diffusion coefficient. It is further seen that the increase of the sodium-ion composition reduces the fluidity of the system. The results highlight the potential of the method and the microscopic description that it can provide to assist the investigation toward a sensible design of IL mixtures as an electrolyte for a high-performance sodium-ion battery.

Using viscoelastic modeling and molecular dynamics based simulations to characterize polymer natural fiber composites

AbstractThe potential for polymer natural fiber composites for manufacturing storage units for products with high ethanol content is explored. The influence of ethanol diffusion into the microstructure of the storage unit on its long‐term mechanical (specifically creep compliance) and viscoelastic properties are measured. Burger's model for polymer viscoelasticity is used to predict durability and other fundamental properties of the composite based on the creep compliance trends. Properties such as the Maxwell moduli and Maxwell viscosities are then modeled as a function of net ethanol uptake and the concentration of natural fiber dispersed phase. Later, a combination of classical molecular dynamics (MD) and semi empirical modeling is used to predict the trends in ethanol diffusion coefficient as a function of temperature and natural fiber concentration. The most efficacious models for this purpose and the ways and means of further improving the simulation accuracy are discussed.

What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD.

Photolyases (PL) and cryptochromes (CRY) are light-sensitive flavoproteins, respectively, involved in DNA repair and signal transduction. Their activation is triggered by an electron transfer process, which partially or fully reduces the photo-activated FAD cofactor. The full reduction additionally requires a proton transfer to the isoalloxazine ring. In plant CRY, an efficient proton transfer takes place within several μs, enabled by a conserved aspartate working as a proton donor, whereas in E. coli PL a proton transfer occurs in the 4 s timescale without any obvious proton donor, indicating the presence of a long-range proton transfer pathway. Unexpectedly, the insertion of an aspartate as a proton donor in a suitable position for proton transfer in E. coli PL does not initiate a transfer process similar to plant CRY, but even prevents the formation of a protonated FAD. In the present work, thanks to a combination of classical molecular dynamics and state-of-the-art DFTB3/MM simulations, we identify a proton transfer pathway from bulk to FAD in E. coli PL associated with a free energy profile in agreement with the experimental kinetics data. The free energy profiles of the proton transfer between aspartate and FAD show an inversion of the driving force between plant CRY and E. coli PL mutants. In the latter, the proton transfer from the aspartate is faster than in plant CRY but also thermodynamically disfavoured, in agreement with the experimental data. Our results further illustrate the fine tuning of the electrostatic FAD environment and the adaptability of the FAD pocket to ensure the divergent functions of the members of the PL-CRY family.

The molecular mechanisms of light adaption in light-harvesting complexes of purple bacteria revealed by a multiscale modeling.

The light-harvesting in photosynthetic purple bacteria can be tuned in response to the light conditions during cell growth. One of the used strategies is to change the energy of the excitons in the major fight-harvesting complex, commonly known as LH2. In the present study we report the first systematic investigation of the microscopic origin of the exciton tuning using three complexes, namely the common (high-light) and the low-light forms of LH2 from Rps. acidophila plus a third complex analogous to the PucD complex from Rps. palustris. The study is based on the combination of classical molecular dynamics of each complex in a lipid membrane and excitonic calculations based on a multiscale quantum mechanics/molecular mechanics approach including a polarizable embedding. From the comparative analysis, it comes out that the mechanisms that govern the adaptation of the complex to different light conditions use the different H-bonding environment around the bacteriochlorophyll pigments to dynamically control both internal and inter-pigment degrees of freedom. While the former have a large effect on the site energies, the latter significantly change the electronic couplings, but only the combination of the two effects can fully reproduce the tuning of the final excitons and explain the observed spectroscopic differences.