A TDDFT investigation of the Photosystem II reaction center: Insights into the precursors to charge separation.

Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments' porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton-charge transfer states (ChlD1+PheD1-)* and (PD2+PD1-)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.

Modulation of cardiac thin filament structure by phosphorylated troponin-I analyzed by protein-protein docking and molecular dynamics simulation.

Tropomyosin, controlled by troponin-linked Ca2+-binding, regulates muscle contraction by a macromolecular scale steric-mechanism that governs myosin-crossbridge-actin interactions. At low-Ca2+, C-terminal domains of troponin-I (TnI) trap tropomyosin in a position on thin filaments that interferes with myosin-binding, thus causing muscle relaxation. Steric inhibition is reversed at high-Ca2+ when TnI releases from F-actin-tropomyosin as Ca2+ and the TnI switch-peptide bind to the N-lobe of troponin-C (TnC). The opposite end of cardiac TnI contains a phosphorylation-sensitive ∼30 residue-long N-terminal peptide that is absent in skeletal muscle, and likely modifies these interactions in hearts. Here, PKA-dependent phosphorylation of serine 23 and 24 modulates Ca2+ and possibly switch-peptide binding to TnC, causing faster relaxation during the cardiac-cycle (lusitropy). The cardiac-specific N-terminal TnI domain is not captured in crystal structures of troponin or in cryo-EM reconstructions of thin filaments; thus, its global impact on thin filament structure and function is uncertain. Here, we used protein-protein docking and molecular dynamics simulation-based protocols to build a troponin model that was guided by and hence consistent with the recent seminal Yamada structure of Ca2+-activated thin filaments. We find that when present on thin filaments, phosphorylated Ser23/24 along with adjacent polar TnI residues interact closely with both tropomyosin and the N-lobe of TnC during our simulations. These interactions would likely bias tropomyosin to an off-state positioning on actin. In situ, such enhanced relaxation kinetics would promote cardiac lusitropy.

Kinetics and Mechanisms of Hydrothermal Dehydration of Cyclic 1,2- and 1,4-Diols.

Hydrothermal dehydration is an attractive method for deoxygenation and upgrading of biofuels because it requires no reagents or catalysts other than superheated water. Although mono-alcohols cleanly deoxygenate via dehydration under many conditions, polyols such as those derived from saccharides and related structures are known to be recalcitrant with respect to dehydration. Here, we describe detailed mechanistic and kinetic studies of hydrothermal dehydration of 1,2- and 1,4-cyclohexanediols as model compounds to investigate how interactions between the hydroxyls can control the reaction. The diols generally dehydrate more slowly and have more complex reaction pathways than simple cyclohexanol. Although hydrogen bonding between hydroxyls is an important feature of the diol reactions, hydrogen bonding on its own does not explain the reduced reactivity. Rather, it is the way that hydrogen bonding influences the balance between the E1 and E2 elimination mechanisms. We also describe the reaction pathways and follow-up secondary reactions for the slower-dehydrating diols.

Large-Scale Distributed Training of Transformers for Chemical Fingerprinting.

Transformer models have become a popular choice for various machine learning tasks due to their often outstanding performance. Recently, transformers have been used in chemistry for classifying reactions, reaction prediction, physiochemical property prediction, and more. These models require huge amounts of data and localized compute to train effectively. In this work, we demonstrate that these models can successfully be trained for chemical problems in a distributed manner across many computers─a more common scenario for chemistry institutions. We introduce MFBERT: Molecular Fingerprints through Bidirectional Encoder Representations from Transformers. We use distributed computing to pre-train a transformer model on one of the largest aggregate datasets in chemical literature and achieve state-of-the-art scores on a virtual screening benchmark for molecular fingerprints. We then fine-tune our model on smaller, more specific datasets to generate more targeted fingerprints and assess their quality. We utilize a SentencePiece tokenization model, where the whole procedure from raw molecular representation to molecular fingerprints becomes data-driven, with no explicit tokenization rules.

Understanding the Solvent Contribution to Chemical Reaction Barriers.

Absolute rate theories attempt to predict the rate constants of reactions from basic principles and independent data. For the contribution of solvent to a reaction rate constant, this requires connecting absolute rate data to fundamental solvent properties such as dielectric constant and refractive index. We have explored this connection for the unimolecular fragmentation reaction of a pinacol radical cation. The rate constants for fragmentation were measured as a function of temperature in 12 different solvents with dielectric constants from 4.7 to 36.2, and the free energies of activation for bond fragmentation in each solvent determined using transition state theory. Using the solvent effects on electron-transfer reactions as a starting point, Marcus theory was used to model the solvent effect on the reaction activation energies. The solvent contribution to both the activation free energy and the overall reaction energy is best described using the Born model rather than the Pekar solvation model. The solvent reorganization energies for bond fragmentation are substantially larger than solvent reorganization energies for electron transfer, presumably because of the requirement to translate the solvent molecules in the course of bond breaking.

Mechanism of Photoinduced Triplet Intermolecular Hydrogen Transfer between Cycloxydim and Chlorothalonil.

The possible reaction mechanisms for the experimentally observed hydrogen transfer between the herbicide cycloxydim (CD) and the triplet fungicide chlorothalonil (CT) were identified with density functional theory (DFT) and time-dependent density function theory (TDDFT) computations. Excited energy transfer (EET) calculations indicate that reactants for intermolecular hydrogen transfer were formed via energy transfer from triplet CT to ground state CD. Three possible reaction pathways after EET were identified, and hydrogen transfer from the hydroxyl group on the cyclohexane ring of CD to CT exhibited the lowest energy barrier. Natural population analysis (NPA) along the reaction pathways has confirmed that the pathways involved either electron transfer induced proton transfer or coupled electron-proton transfer, leading to different potential energy profiles. Electrostatic potential (ESP) study substantiated the reaction mechanisms in different pathways. This study suggests an explanation for the accelerated photodegradation of CD by CT and provides a pipeline for future studies of photoinduced intermolecular hydrogen transfer.

Sphalerite is a geochemical catalyst for carbon-hydrogen bond activation.

Reactions among minerals and organic compounds in hydrothermal systems are critical components of the Earth's deep carbon cycle, provide energy for the deep biosphere, and may have implications for the origins of life. However, there is limited information as to how specific minerals influence the reactivity of organic compounds. Here we demonstrate mineral catalysis of the most fundamental component of an organic reaction: the breaking and making of a covalent bond. In the absence of mineral, hydrothermal reaction of cis- and trans-1,2-dimethylcyclohexane is extremely slow and generates many products. In the presence of sphalerite (ZnS), however, the reaction rate increases dramatically and one major product is formed: the corresponding stereoisomer. Isotope studies show that the sphalerite acts as a highly specific heterogeneous catalyst for activation of a single carbon-hydrogen bond in the dimethylcyclohexanes.

Troponin structure: its modulation by Ca(2+) and phosphorylation studied by molecular dynamics simulations.

The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 µs) and bisphosphorylated (SP23/SP24) cTn (9 µs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.

Simulation of lipid bilayer self-assembly using all-atom lipid force fields.

In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.

Organic Oxidations Using Geomimicry.

Oxidations of phenylacetic acid to benzaldehyde, benzyl alcohol to benzaldehyde, and benzaldehyde to benzoic acid have been observed, in water as the solvent and using only copper(II) chloride as the oxidant. The reactions are performed at 250 °C and 40 bar, conditions that mimic hydrothermal reactions that are geochemically relevant. Speciation calculations show that the oxidizing agent is not freely solvated copper(II) ions, but complexes of copper(II) with chloride and carboxylate anions. Measurements of the reaction stoichiometries and also of substituent effects on reactivity allow plausible mechanisms to be proposed. These oxidation reactions are relevant to green chemistry in that they proceed in high chemical yield in water as the solvent and avoid the use of toxic heavy metal oxidizing reagents.

Imaging phase separation in model lipid membranes through the use of BODIPY based molecular rotors.

In order to fully understand the dynamics of processes within biological lipid membranes, it is necessary to possess an intimate knowledge of the physical state and ordering of lipids within the membrane. Here we report the use of three molecular rotors based on meso-substituted boron-dipyrrin (BODIPY) in combination with fluorescence lifetime spectroscopy to investigate the viscosity and phase behaviour of model lipid bilayers. In phase-separated giant unilamellar vesicles, we visualise both liquid-ordered (Lo) and liquid-disordered (Ld) phases using fluorescence lifetime imaging microscopy (FLIM), determining their associated viscosity values, and investigate the effect of composition on the viscosity of these phases. Additionally, we use molecular dynamics simulations to investigate the orientation of the BODIPY probes within the bilayer, as well as using molecular dynamics simulations and fluorescence correlation spectroscopy (FCS) to compare diffusion coefficients with those predicted from the fluorescence lifetimes of the probes.

Hydrothermal photochemistry as a mechanistic tool in organic geochemistry: the chemistry of dibenzyl ketone.

Hydrothermal organic transformations under geochemically relevant conditions can result in complex product mixtures that form via multiple reaction pathways. The hydrothermal decomposition reactions of the model ketone dibenzyl ketone form a mixture of reduction, dehydration, fragmentation, and coupling products that suggest simultaneous and competitive radical and ionic reaction pathways. Here we show how Norrish Type I photocleavage of dibenzyl ketone can be used to independently generate the benzyl radicals previously proposed as the primary intermediates for the pure hydrothermal reaction. Under hydrothermal conditions, the benzyl radicals undergo hydrogen atom abstraction from dibenzyl ketone and para-coupling reactions that are not observed under ambient conditions. The photochemical method allows the primary radical coupling products to be identified, and because these products are generated rapidly, the method also allows the kinetics of the subsequent dehydration and Paal-Knorr cyclization reactions to be measured. In this way, the radical and ionic thermal and hydrothermal reaction pathways can be studied separately.

Modulation of Structure and Dynamics of Cardiac Troponin by Phosphorylation and Mutations Revealed by Molecular Dynamics Simulations.

Adrenaline acts on ß1 receptors in the heart muscle to enhance contractility, increase the heart rate, and increase the rate of relaxation (lusitropy) via activation of the cyclic AMP-dependent protein kinase, PKA. Phosphorylation of serines 22 and 23 in the N-terminal peptide of cardiac troponin I is responsible for lusitropy. Mutations associated with cardiomyopathy suppress the phosphorylation-dependent change. Key parts of troponin responsible for this modulatory system are disordered and cannot be resolved by conventional structural approaches. We performed all-atom molecular dynamics simulations (5 × 1.5 µs runs) of the troponin core (419 amino acids) in the presence of Ca2+ in the bisphosphorylated and unphosphorylated states for both wild-type troponin and the troponin C (cTnC) G159D mutant. PKA phosphorylation affects troponin dynamics. There is significant rigidification of the structure involving rearrangement of the cTnI(1-33)-cTnC interaction and changes in the distribution of the cTnC helix A/B angle, troponin I (cTnI) switch peptide (149-164) docking, and the angle between the regulatory head and ITC arm domains. The familial dilated cardiomyopathy cTnC G159D mutation whose Ca2+ sensitivity is not modulated by cTnI phosphorylation exhibits a structure inherently more rigid than the wild type, with phosphorylation reversing the direction of all metrics relative to the wild type.

Understanding the relative affinity and specificity of the pleckstrin homology domain of protein kinase B for inositol phosphates.

Protein kinase B (PKB) is a serine/threonine kinase that plays a key role in the phosphoinositide 3-kinase (PI3K) pathway-one of the most frequently activated proliferation pathways in cancer. In this pathway, PKB is recruited to the plasma membrane by direct interaction of its pleckstrin homology (PH) domain with the inositol phosphate head-group of phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P(3)] or phosphatidylinositol 3,4-bisphosphate [PtdIns(3,4)P(2)]. This recruitment is a critical stage in the activation of PKB, whose downstream effectors play important roles in cell survival, proliferation and growth. It is therefore of great interest to understand PKB's mode of binding, as well as its specificity and affinity for different phosphoinositides. We have used a total of 3 µs of molecular dynamics (MD) simulations to better understand the interactions of the PKB PH domain with the inositol phosphate head-groups of phosphoinositides involved in the PI3K pathway. Our computational models successfully mirror PKB's in vivo selectivity for 3-phosphorylated phosphoinositides. Furthermore, the models also help to rationalize unexpected in vitro data in which inositol 1,4,5-trisphosphate [Ins(1,4,5)P(3)] binds with a relatively high affinity to the PKB PH domain, despite its parent lipid phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] being known not to bind in vivo. With the support of computational simulations, we propose that when not bonded to a phosphatidate tail Ins(1,4,5)P(3) binds in an orientation in which its inositol ring is flipped with respect to the 3-phosphorylated inositol phosphate ligands and its parent lipid.

Lipid21: Complex Lipid Membrane Simulations with AMBER.

We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell membrane lipid compositions, including raft-like domains. Head group torsion parameters are revised, resulting in improved agreement with NMR order parameters, and hydrocarbon chain parameters are updated, providing a better match with phase transition temperature. Extensive validation runs (0.9 µs per lipid type) show good agreement with experimental measurements. Furthermore, the simulation of raft-like bilayers demonstrates the perturbing effect of increasing PUFA concentrations on cholesterol molecules. The force field derivation is consistent with the AMBER philosophy, meaning it can be easily mixed with protein, small molecule, nucleic acid, and carbohydrate force fields.

A theoretical investigation of inositol 1,3,4,5-tetrakisphosphate.

This paper describes the parameterization of inositol 1,3,4,5-tetrakisphosphate [Ins(1,3,4,5)P(4)] for use in molecular dynamics (MD) simulations. For this theoretical investigation, eleven isomers of Ins(1,3,4,5)P(4), with different levels and arrangements of protonation, have been considered. Herein we report accurate quantum mechanics (QM) calculations offering a detailed description of the energetic and structural properties of the Ins(1,3,4,5)P(4) isomers and subsequent development of parameters for these isomers for application in the AMBER force field. QM calculations were employed to geometry optimize the Ins(1,3,4,5)P(4) isomers, using the DFT-B3LYP level of theory in gas phase. In subsequent steps, charge parameters were generated for each isomer. These charge parameters, plus assigned atom-types from the AMBER ff99SB force field, were then applied to the optimized isomers for energy minimization in AMBER. The quality of the parameters was evaluated by comparing the structural, energetic and spectroscopic properties of the Ins(1,3,4,5)P(4) isomers between the QM geometry optimization stage, from which the parameters were generated, and the energy minimization stage, in which the parameters were applied. The results were shown to be in strong qualitative agreement between these stages, suggesting good quality parameters have been obtained. Additionally, adaptations to the gas phase protocol, investigating the use of the MP2 method for the geometry optimization stage and GAFF atom-types for the energy minimization stage, were tested. These results confirmed the initial protocol applied was the most appropriate. Calculations for the Ins(1,3,4,5)P(4) isomers were also carried out in the presence of implicit solvent, allowing comparison and validation of the theoretical calculations with experimental data. The computed energetic properties of the Ins(1,3,4,5)P(4) isomers were assessed against their experimental probabilities based on (31)P-NMR titration data. The computational and experimental results were shown to be in strong agreement, with the lower energy isomers corresponding to those more probable. This paper reports a clearly-defined algorithmic approach to generate parameters for the highly charged Ins(1,3,4,5)P(4) ligand, permitting their use in future MD studies.

Further evaluation of quantum chemical methods for the prediction of non-specific binding of positron emission tomography tracers.

The non-specific binding of candidate positron emission tomography (PET) radiotracers causes resulting PET images to have poor contrast and is a key determinant for the success or failure of imaging drugs. Non-specific binding is thought to arise when radiotracers bind to cell membranes and moieties other than their intended target. Our previous preliminary work has proposed the use of the drug-lipid interaction energy descriptor to predict the level of non-specific binding in vivo using a limited set of ten well known PET radiotracers with kinetic modelling data taken from the literature. This work validates and extends the use of the drug-lipid interaction energy descriptor using a new set of twenty-two candidate PET radiotracers with non-specific binding data recently collected at the same imaging centre with consistent methodology. As with the previous set of radiotracers, a significant correlation is found between the quantum chemical drug-lipid interaction energy and in vivo non-specific binding experimental values. In an effort to speed up the calculation process, several semi-empirical quantum chemical methods were assessed for their ability to reproduce the ab initio results. However no single semi-empirical method was found to consistently reproduce the level of correlation achieved with ab initio quantum chemical methods.

Experimental exploration of the Mulliken-Hush relationship for intramolecular electron transfer reactions.

The Mulliken-Hush (M-H) relationship provides the critical link between optical and thermal electron transfer processes, and yet very little direct experimental support for its applicability has been provided. Dicyanovinylazaadamantane (DCVA) represents a simple two-state (neutral/charge-transfer) intramolecular electron transfer system that exhibits charge-transfer absorption and emission spectra that are readily measurable in solvents with a wide range of polarities. In this regard it represents an ideal model system for studying the factors that control both optical charge separation (absorption) and recombination (emission) processes in solution. Here we explore the applicability of the M-H relation to quantitative descriptions of the optical charge-transfer processes in DCVA. For DCVA, the measured radiative rate constants exhibit a linear dependence on transition energy, and transition dipole moments exhibit an inverse dependence on transition energy, consistent with the M-H relationship.

Protein identification and quantification by two-dimensional infrared spectroscopy: implications for an all-optical proteomic platform.

Electron-vibration-vibration two-dimensional coherent spectroscopy, a variant of 2DIR, is shown to be a useful tool to differentiate a set of 10 proteins based on their amino acid content. Two-dimensional vibrational signatures of amino acid side chains are identified and the corresponding signal strengths used to quantify their levels by using a methyl vibrational feature as an internal reference. With the current apparatus, effective differentiation can be achieved in four to five minutes per protein, and our results suggest that this can be reduced to <1 min per protein by using the same technology. Finally, we show that absolute quantification of protein levels is relatively straightforward to achieve and discuss the potential of an all-optical high-throughput proteomic platform based on two-dimensional infrared spectroscopic measurements.

Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis.

In the last 10 years, several forms of two-dimensional infrared (2DIR) spectroscopy have been developed, such as IR pump-probe spectroscopy and photon-echo techniques. In this Account, we describe a doubly vibrationally enhanced four-wave mixing method, in which a third-order nonlinear signal is generated from the interaction of two independently tunable IR beams and an electron-polarizing visible beam at 790 nm. When the IR beams are independently in resonance with coupled vibrational transitions, the signal is enhanced and cross-peaks appear in the spectrum. This method is known as either DOVE (doubly vibrationally enhanced) four-wave mixing or EVV (electron-vibration-vibration) 2DIR spectroscopy. We begin by discussing the basis and properties of EVV 2DIR. We then discuss several biological and potential biomedical applications. These include protein identification and quantification, as well as the potential of this label-free spectroscopy for protein and peptide structural analysis. In proteomics, we also show how post-translational modifications in peptides (tyrosine phosphorylation) can be detected by EVV 2DIR spectroscopy. The feasibility of EVV 2DIR spectroscopy for tissue imaging is also evaluated. Preliminary results were obtained on a mouse kidney histological section that was stained with hematoxylin (a small organic molecule). We obtained images by setting the IR frequencies to a specific cross-peak (the strongest for hematoxylin was obtained from its analysis in isolation; a general CH(3) cross-peak for proteins was also used) and then spatially mapping as a function of the beam position relative to the sample. Protein and hematoxylin distribution in the tissue were measured and show differential contrast, which can be entirely explained by the different tissue structures and their functions. The possibility of triply resonant EVV 2DIR spectroscopy was investigated on the retinal chromophore at the centre of the photosynthetic protein bacteriorhodopsin (bR). By putting the visible third beam in resonance with an electronic transition, we were able to enhance the signal and increase the sensitivity of the method by several orders of magnitude. This increase in sensitivity is of great importance for biological applications, in which the number of proteins, metabolites, or drug molecules to be detected is low (typically pico- to femtomoles). Finally, we present theoretical investigations for using EVV 2DIR spectroscopy as a structural analysis tool for inter- and intramolecular interaction geometries.