Force Field Optimization using Dynamics and Ensemble Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO

Capturing ultrafast energy flow of a heme protein in crowded milieu

Energy flow in biomolecules is a dynamic process vital for understanding health, disease, and applications in biotechnology and medicine. In crowded environments, where biomolecular functions are modulated, comprehending energy flow becomes crucial for accurately understanding cellular processes like signaling and subsequent functions. This study employs ultrafast transient absorption spectroscopy to demonstrate energy funneling from the photoexcited heme of bovine heart cytochrome c to the protein exterior, in the presence of common synthetic (Dextran 40, Ficoll 70, PEG 8 and Dextran 70) and protein-based (BSA and β-LG) crowders. The through-space energy transfer mode for ferric and the methionine rebinding mode for ferrous cytochrome c show the strongest solvent coupling. The heterogeneous behaviour of crowders, influenced by crowder-protein interactions and caging effects at certain higher concentrations, reveal diverse trends. Notably, protein crowders perturb all transport routes of vibrational energy transfer, causing delays in energy transfer processes. These findings provide significant insights into the basic tenets of energy flow, one of the most fundamental processes, in crowded cellular environments.

Importance of clustering Improve of Modified Bee Colony Optimization (MBCO) algorithm by optimizing the clusters initial values

The modified bee colony algorithm is one of the excellent methods that has been proposed in recent years for data clustering. This MBCO algorithm randomly values the primary centers of the cluster by selecting a number of data from the data set, which makes the algorithm sensitive to the presence of noise and outgoing data in the data set and reduces its performance. Therefore, to solve this problem, the proposed method used three approaches to quantify the initial centers of the clusters. In the proposed method, first the initial centers of the clusters are generated by chaos methods, KMeans++algorithm and KHM algorithm to determine the optimal position for the centers. Then the MBCO algorithm starts working with these centers. The performance of the proposed method compared to a number of other clustering methods was evaluated on 7 UCI datasets based on 6 clustering evaluation criteria. For example, in the iris data set, the proposed method with chaos approaches, KHM and KMeans++with accuracy of 0.8725, 0.8737 and 0.8725, respectively, and the MBCO method with accuracy of 0.8678, and in terms of CH criteria, the proposed method with chaotic approaches, KHM and KMeans++reached values of 0.3901, 0.54848, 0.5147 and MBCO method of 0.3620, respectively. Better achieved. In general, the results of the experiments according to the 6 evaluation criteria showed better performance of the proposed method compared to other methods in most data sets according to the 6 evaluation criteria.

Quasi-Static Two-Dimensional Infrared Spectra of the Carboxyhemoglobin Subsystem under Electric Fields: A Theoretical Study

There is no doubt that electric fields of a specific frequency and intensity could excite certain vibrational modes of a macromolecule, which alters its mode coupling and conformation. Motivated by recent experiments and theories, we study the mode coupling between the Fe-CO mode and CO-stretch mode and vibration energy transfer among the active site and proteins in carboxyhemoglobin (HbCO) under different electric fields using the quasi-static two-dimensional infrared spectra. This study uses iron-porphyrin-imidazole-CO and two distal histidines in HbCO as the subsystem. The potential energy and dipole moment surfaces of the subsystem are calculated using an all-electron ab initio (B3LYP-D3(BJ)) method with the basis set Lanl2dz for the Fe atom and 6-31G(d,p) for C, H, O, and N atoms. Although the subsystem is reduced dimensionally, the anharmonic frequency and anharmonicity of the CO-stretch mode show excellent agreement with experimental values. We use the revealing noncovalent interaction method to confirm the hydrogen bond between the H_ε atom of the His63 and the CO molecule. Our study confirms that the mode coupling between the Fe-CO mode and CO-stretch mode does not exist when the subsystem is free of electric field perturbation, which is coupled when the electric field is -0.5142 V/nm. In addition, with the increases of distance between the active site and the His92, there is no vibrational energy transfer between them when the electric field is 1.028 V/nm. We believe that our work could provide new ideas for increasing the dissociation efficiency of the Fe-CO bond and theoretical references for experimental research.

Microstructures of the Sulfonic Acid-Functionalized Ionic Liquid/Sulfuric Acid and Their Interactions: A Perspective from the Isobutane Alkylation

The all-atom force field for concentrated sulfuric acid (98.30 wt %) was developed in this work based on ab initio calculations. The structural and dynamical properties of sulfuric acid and the mixing behaviors of sulfuric acid with ionic liquids (ILs), i.e., SFIL (1-methyl-3-(propyl-3-sulfonate) imidazolium bisulfate ([PSMim][HSO₄])) and non-SFIL (1-methyl-3-propyl imidazolium bisulfate ([PMim][HSO₄])), were investigated using a molecular dynamics simulation. For sulfuric acid, most H₃O⁺ ions were found beside HSO₄^- ions, forming a contact ion pair with the HSO₄^- ions, and three-dimensional hydrogen-bonding networks existed in the sulfuric acid. Analyses indicate that both ILs could be miscible with sulfuric acid with a strong exothermic character. The new strong interaction site between the sulfonic acid group of SFIL and an H₂SO₄ molecule through a strong hydrogen-bonding interaction was observed, which was beneficial to the catalytic activity and stability of the sulfuric acid. This observation is in good agreement with the experimental results that indicate SFILs could enhance the reusability of sulfuric acid for the isobutane alkylation about 4-fold compared to that of non-SFILs. Hopefully this work will provide insights into the screening and designing of new isobutane alkylation catalysts based on sulfuric acid and SFILs.

Ultrafast Dynamics of Carboxy-Hemoglobin: Two-Dimensional Infrared Spectroscopy Experiments and Simulations

This Letter presents a comparison between experimental and simulated 2D mid-infrared spectra of carboxy-hemoglobin in the spectral region of the carbon monoxide stretching mode. The simulations rely on a fluctuating potential energy surface that includes both the effect of heme and the protein surroundings computed from molecular dynamics simulations. A very good agreement between theory and experiment is obtained with no adjustable parameters. The simulations show that the effect of the distal histidine through the hydrogen bond is strong and is directly responsible for the slow decay of the frequency-frequency correlation function on a 10 ps time scale. This study confirms that fluctuations in carboxy-hemoglobin are more inhomogeneous than those in the more frequently studied carboxy-myoglobin. The comparison between simulations and experiments brings valuable information on the complex relation between protein structure and spectral diffusion.

Vibrational ladder climbing in carboxy-hemoglobin: effects of the protein environment

We present simulations on vibrational ladder climbing in carboxy-hemoglobin. Motivated by recent experiments, we study the influence of different realistic pump probe parameters. To allow for a direct comparison with experimental results, transient absorption spectra obtained by a weak probe pulse following the strong, shaped pump pulse are calculated. The influence of the protein fluctuations is taken into account using a recently developed microscopic model. This model consists of a quantum Hamiltonian describing the CO vibration in carboxy-hemoglobin, together with a fluctuating potential, which is obtained by electronic structure calculation based on a large number of protein configurations. Using realistic pulse parameters, vibrational excitations to very high-lying states are possible, in qualitative agreement with experimental observations.

CO-dynamics in the active site of cytochrome c oxidase

The transfer of CO from heme a3 to the Cu(B) site in Cytochrome c oxidase (CcO) after photolysis is studied using molecular dynamics simulations using an explicitly reactive, parametrized potential energy surface based on density functional theory calculations. After photodissociation from the heme-Fe, the CO ligand rebinds to the Cu(B) site on the sub-picosecond time scale. Depending on the simulation protocol the characteristic time ranges from 260 fs to 380 fs which compares with an estimated 450 fs from experiment based on the analysis of the spectral changes as a function of time delay after the photodissociating pulse. Following photoexcitation ≈90% of the ligands are found to rebind to either the Cu(B) (major component, 85%) or the heme-Fe (minor component, 2%) whereas about 10% remain in an unbound state. The infrared spectra of unbound CO in the active site is broad and featureless and no appreciable shift relative to gas-phase CO is found, which is in contrast to the situation in myoglobin. These observations explain why experimentally, unbound CO in the binuclear site of CcO has not been found as yet.

Vibrational relaxation and energy migration of N-methylacetamide in water: the role of nonbonded interactions

Nonequilibrium molecular dynamics (MD) simulations together with physics-based force fields are used to follow energy flow between vibrationally excited N-methylacetamide (NMA) and water. The simulations are carried out with a previously validated force field for NMA, based on a multipolar representation of the electrostatics, and with a new fluctuating point charge model. For the water solvent, a flexible and a rigid model was employed to distinguish between the role of inter- and intramolecular degrees of freedom. On a 10 ps time scale about 90% of the available energy goes into the solvent. The remaining energy resides within internal NMA-degrees of freedom from where energy flow takes place on longer time scales. The total amount of energy transferred to the solvent on the 10 ps time scale does not depend on whether the water molecules are rigid or flexible during the simulations. Vibrational energy relaxation time scales include two regimes: one on the several 100 fs time scale and a longer one, ranging from 6 to 10 ps. This longer time scale agrees with previous simulations but overestimates the experimentally determined relaxation time by a factor of 2, which can be explained by the classical treatment of the vibrations. Including a previously determined quantum correction factor brings the long time scale into quite favorable agreement with experiment. Coupling to the bending vibration of the water molecules in H-bonding contact with the excited C═O chromophore is substantial. The equilibrium and nonequilibrium distribution of the bending angles of the water molecules in contact with the local oscillator are non-Gaussian, and one approaches the other on the subpicosecond time scale. Analysis of the water velocity distribution suggests that the C═O vibrational energy relaxes into the solvent water shells in an impulsive fashion on a picosecond time scale.

Multisurface Adiabatic Reactive Molecular Dynamics

Adiabatic reactive molecular dynamics (ARMD) simulation method is a surface-crossing algorithm for modeling chemical reactions in classical molecular dynamics simulations using empirical force fields. As the ARMD Hamiltonian is time dependent during crossing, it allows only approximate energy conservation. In the current work, the range of applicability of conventional ARMD is explored, and a new multisurface ARMD (MS-ARMD) method is presented, implemented in CHARMM and applied to the vibrationally induced photodissociation of sulfuric acid (H2SO4) in the gas phase. For this, an accurate global potential energy surface (PES) involving 12 H2SO4 and 4 H2O + SO3 force fields fitted to MP2/6-311G++(2d,2p) reference energies is employed. The MS-ARMD simulations conserve total energy and feature both intramolecular H-transfer reactions and water elimination. An analytical treatment of the dynamics in the crossing region finds that conventional ARMD can approximately conserve total energy for limiting cases. In one of them, the reduced mass of the system is large, which often occurs for simulations of solvated biomolecular systems. On the other hand, MS-ARMD is a general approach for modeling chemical reactions including gas-phase, homogeneous, heterogeneous, and enzymatic catalytic reactions while conserving total energy in atomistic simulations.

Toward force fields for atomistic simulations of iridium-containing complexes

The structural and energetic characterization of metal complexes is important in catalysis and photochemical applications. Unraveling their modes-of-action can be greatly assisted by computation, which typically is restricted to computationally demanding methods including electronic structure calculations with density functional theory. Here, we present an empirical force field based on valence bond theory applicable to a range of octahedral Ir(III) complexes with different coordinating ligands, including iridium complexes with a chiral P,N ligand. Using an approach applicable to metal-containing complexes in general, it is shown that with one common parametrization 85% of the 116 diastereomers--all within 21 kcal/mol of the lowest energy conformation of each series--can be correctly ranked. For neutral complexes, all diastereomers are ranked correctly. This helps to identify the most relevant diastereomers which, if necessary, can be further investigated by more demanding computational methods. Furthermore, if one specific complex is considered, the root mean square deviation between reference data from electronic structure calculations and the force field is ≈1 kcal/mol. This, together with the possibility to carry out explicit simulations in solution paves the way for an atomistic understanding of iridium-containing complexes in catalysis.

Vibrationally induced dissociation of sulfuric acid (H2SO4)

One of the important reactive steps in Earth's atmosphere is the decomposition of H(2)SO(4) to H(2)O and SO(3). However, because the UV spectrum of H(2)SO(4) was not found up to 140 nm, alternative mechanisms, including vibrationally induced dissociation, were proposed. Using adiabatic reactive molecular dynamics (ARMD) simulations with validated force fields for the product and educt channels, it is shown through explicit atomistic simulation that by exciting the ν(9) (OH-stretching-) mode, photodissociation can occur on the picosecond time scale. With the potential energy surfaces used in the present work, ν(9) = 4 is sufficient for this process. From a statistically significant number of trajectories (several thousands), vibrationally induced dissociation times are found to follow Gamma-distributions with most likely reaction times between 40 and 200 ps by depositing energies ranging from 40 to 60 kcal/mol, corresponding to 4 and 6 vibrational quanta in the OH stretching vibration. Because ARMD simulations allow multiple and long-time simulations, both nonstatistical, impulsive H-transfer and statistical, IVR-regimes of the decomposition reaction can be discussed in detail at an atomistic level.

A generalized reactive force field for nonlinear hydrogen bonds: hydrogen dynamics and transfer in malonaldehyde

Using molecular dynamics (MD) simulations, the spectroscopy and dynamics of malonaldehyde is investigated. To this end, the recently proposed molecular mechanics with proton transfer (MMPT) potential is generalized to nonlinear hydrogen bonds. The calculated properties for malonaldehyde in both gas and condensed phases, including equilibrium geometries, infrared spectra, tunneling splittings, and hydrogen transfer rates, compare well with previous experimental and computational works. In particular, by using a harmonic bath averaged (HBA) Hamiltonian, which is based on a reaction path Hamiltonian, it is possible to estimate the tunneling splitting in an efficient manner. It is found that a zero point corrected barrier of 6.7 kcal/mol and effective masses of 1.234 (i.e., 23.4% larger than the mass of a physical H-atom) and 1.117 (for the physical D-atom) are consistent with the measured splittings of 21.6 and 2.9 cm(-1), respectively. The HBA Hamiltonian also yields a pair of hydrogen transfer fundamentals at 1573 and 1267 cm(-1), similar to results obtained with a reaction surface Hamiltonian on a MP2/6-31G(**) potential energy surface. This amounts to a substantial redshift of more than 1000 cm(-1) which can be rationalized by comparison with weakly (HCO(+): rare gas) and strongly (H(2)O-H(+)-OH(2)) proton-bound systems. Hydrogen transfer rates in vacuum and water were determined from the validated MMPT potential and it is found that the solvent enhances the rate by a factor of 5 at 300 K. The rates of 2.4/ns and 10/ns are commensurate with previous density functional tight binding ab initio MD studies.