Severe neonatal thrombocytopenia due to anti-HPA-4b alloantibodies: Third report described in a Caucasian mother.

BACKGROUND: Fetal and Neonatal Alloimmune Thrombocytopenia (FNAIT) results from maternal platelet alloimmunization against paternal antigens inherited by the fetus, most often due to the Human Platelet Antigen (HPA)-1 system in Caucasians. We investigated in 2023, a 30-year-old Caucasian woman Gravida 2 Para 1 who gave birth at 35 weeks of gestation to a male (body weight 2210 g) without signs of bleeding. A severe thrombocytopenia (platelet count at 3 G/L) was discovered incidentally a few hours after delivery in the context of the management of a respiratory distress. The newborn recovered after one platelet concentrate transfusion and normalized his platelet count at Day 5. STUDY DESIGN AND METHODS: FNAIT investigation was performed according to guideline recommendations. Platelet genotyping was carried out by multiplex PCR. Maternal serological investigation included Monoclonal Antibody-specific Immobilization of Platelet Antigens method (MAIPA) and Luminex technology. RESULTS: Parental and newborn genotyping pointed out an HPA-4 incompatibility between the mother and the newborn and the father. Serological investigation revealed an anti-HPA-4b alloantibody confirming the diagnosis of neonatal alloimmune thrombocytopenia. CONCLUSION: We described the third case of anti-HPA-4b alloantibody discovered in a Caucasian mother. This case strengthens the need for reference laboratory to genotype a panel of HPA alleles reflecting local genetic population diversity and for crossmatch of maternal serum with fresh paternal platelets in clinical suspected cases of neonatal alloimmune thrombocytopenia.

Automatic Rhodopsin Modeling with Multiple Protonation Microstates.

Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.

Solvent Effects and pH Dependence of the X-ray Absorption Spectra of Proline from Electrostatic Embedding Quantum Mechanics/Molecular Mechanics and Mixed-Reference Spin-Flip Time-dependent Density-Functional Theory.

The accurate description of solvent effects on X-ray absorption spectra (XAS) is fundamental for comparing the simulated spectra with experiments in solution. Currently, few protocols exist that can efficiently reproduce the effects of the solute/solvent interactions on XAS. Here, we develop an efficient and accurate theoretical protocol for simulating the solvent effects on XAS. The protocol combines electrostatic embedding QM/MM based on electrostatic potential fitted operators for describing the solute/solvent interactions and mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) for simulating accurate XAS spectra. To demonstrate the capabilities of our protocol, we compute the X-ray absorption of neutral proline in the gas phase and ionic proline in water in all relevant K-edges, showing excellent agreement with experiments. We show that states represented by core to π* transitions are almost unaffected by the interaction with water, whereas the core to σ* transitions are more impacted by the fluctuation of proline structure and the electrostatic interaction with the solvent. Finally, we reconstruct the pH-dependent XAS of proline in solution, determining that the N K-edge can be used to distinguish its three protonation states.

An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators.

Hybrid quantum mechanics/molecular mechanics (QM/MM) models are successful at describing the properties and reactivity of biological macromolecules. Combining ab initio QM/MM methods and periodic boundary conditions (PBC) is currently the optimal approach for modeling chemical processes in an infinite environment, but frequently, these models are too time-consuming for general applicability to biological systems in a solution. Here, we define a simple and efficient electrostatic embedding QM/MM model in PBC, combining the benefits of electrostatic potential fitted atomic charges and particle-mesh Ewald sums, which can efficiently treat systems of an arbitrary size at a reasonable computational cost. To illustrate this, we apply our scheme to extract the lowest singlet excitation energies from a model for Arabidopsis thaliana cryptochrome 1 containing circa 93 000 atoms, accurately reproducing the experimental absorption maximum.

Stressing the differences in alizarin and purpurin dyes through UV-visible light absorption and 1H-NMR spectroscopies.

Three anthraquinone-based chromophores (9,10-anthraquinone, alizarin, purpurin) are compared from the point of view of their experimental and computed NMR and UV-visible light absorption spectra. Using a hybrid (explicit/implicit) solvent model, each proton chemical shift can be reproduced with an error of less than 7%, even when such protons are engaged in inter-molecular hydrogen bonds with the solvent or when the analyzed sample contains a significant amount of impurities, for instance, 9,10-anthraquinone in purpurin. All the steady-state UV-visible absorption spectra feature a significant vibrational progression in the first absorption band. The shape of the corresponding computed spectra, including vibronic couplings obtained with the adiabatic Hessian approach and the Franck-Condon and Herzberg-Teller approximation of the transition dipole, are in excellent agreement with the experimental ones. The importance and the nature of the vibronic couplings are different for the three molecules, even if they only differ by the number of hydroxyl groups.

Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome.

Infrared (IR) spectroscopy is an undoubtedly valuable tool for analyzing vibrations, conformational changes, and chemical reactions of biological macromolecules. Currently, there is a lack of theoretical methods to create a model successfully and efficiently simulate and interpret the origin of the spectral signatures, which are often complex to analyze. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the IR spectrum, the method can provide the origin of each peak from clearly identified molecular motions of constituent fragments. As a proof of concept, we analyze the IR spectra of flavin adenine dinucleotides in water and in Arabidopsis thaliana cryptochrome proteins for four redox forms, in addition to the difference IR spectra before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N-H hydrogen out-of-plane motions and hydrogen bendings.

Chemi- and Bioluminescence of Cyclic Peroxides.

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

UV-visible absorption spectrum of FAD and its reduced forms embedded in a cryptochrome protein.

Cryptochromes are a class of flavoproteins proposed as candidates to explain magnetoreception of animals, plants and bacteria. The main hypothesis is that a biradical is formed upon blue-light absorption by flavin adenine dinucleotide (FAD). In a protein milieu, the oxidized form of FAD can be reduced, leading to four redox derivative forms: anionic and neutral semi-reduced radicals, and anionic and neutral fully reduced forms. All these forms have a characteristic electronic absorption spectrum, with a strong vibrational resolution. Here, we carried out a normal mode analysis at the electrostatic embedding QM/MM level of theory to compute the vibrationally resolved absorption spectra of the five redox forms of FAD embedded in a plant cryptochrome. We show that explicitly accounting for vibrational broadening contributions to electronic transitions is essential to reproduce the experimental spectra. In the case of the neutral radical form of FAD, the absorption spectrum is reproduced only if the presence of a tryptophan radical is considered.

pH-Dependent absorption spectrum of oxyluciferin analogues in the active site of firefly luciferase.

In the quest for the identification of the light emitter(s) responsible for the firefly bioluminescence, the study of oxyluciferin analogues with controlled chemical and electronic structures is of particular importance. In this article, we report the results of our experimental and computational investigation of the pH-dependent absorption spectra characterizing three analogues bound into the luciferase cavity, together with adenosine-monophosphate (AMP). While the analogue microscopic pKa values do not differ much from their reference values, it turns out that the AMP protonation state is analogue-dependent and never doubly-deprotonated. A careful analysis of the interactions evidences the main role of E344 glutamic acid, as well as the flexibility of the cavity which can accommodate any oxyluciferin analogue. The consideration of the absorption spectra suggests that the oxyluciferin enolate form has to be excluded from the list of the bioluminescence reaction products.

Improved evaluation of spin-polarization energy contributions using broken-symmetry calculations.

Spin-polarization effects may play an important role in free radicals and in the magnetic coupling between radical centers. Starting from restricted open-shell calculations, i.e., a closed-shell description of the non-magnetic core electrons, a low-order perturbation expansion identifies the spin-polarization contribution to the energy of mono-radicals and to singlet-triplet energy differences in diradicals. Broken-symmetry (BS) single-determinant calculations introduce only a fraction of spin-polarization effects, and in a biased manner, since BS determinants are not spin eigenfunctions. We propose a simple technique to correctly evaluate spin-polarization energies by taking into account the effect of spin-flip components on one-hole one-particle excited configurations. Spin-decontamination corrections are shown to play a non-negligible role in the BS evaluation of bond energies. The importance of spin decontamination is illustrated in cases for which spin polarization is the leading contribution to the singlet-triplet gap, which characterizes twisted conjugated double bonds and disjoint diradicals.

Modern quantum chemistry with [Open]Molcas.

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

Analytic QM/MM atomic charge derivatives avoiding the scaling of coupled perturbed equations with the MM subsystem size.

In electrostatic embedding mixed quantum and molecular mechanics (QM/MM) approaches, the QM charge distribution is polarized by the electrostatic interaction with the MM environment. Analytic derivatives of expectation values of operators are required to extract properties such as vibrational spectra. These derivatives usually require solving a set of coupled perturbed equations for each nucleus/atom in the system, thus becoming prohibitive when the MM subsystem contains thousands of atoms. In the context of Electrostatic Potential Fitting (ESPF) QM/MM, we can easily overcome this bottleneck by defining a set of auxiliary coupled perturbed equations called the Q-vector equations. The Q-vector method scales only with the size of the QM subsystem, producing an effective charge tensor that leads to the atomic charge derivative after contraction with the MM electrostatic potential gradient. As an example, we use the charge derivatives as an analysis tool to identify the most important chromophore-polarizing amino-acids in plant cryptochrome. This finding opens up the route of defining polarizable force fields and simulating vibrational spectroscopy using ESPF QM/MM electrostatic embedding at an affordable computational cost.

Chemical Tuning of Magnetic Exchange Couplings Using Broken-Symmetry Density Functional Theory.

With broken-symmetry Kohn-Sham density functional theory calculations, it is demonstrated that the ferromagnetic or anti-ferromagnetic character of two prototypical binuclear copper complexes can be modified, both in the sign and in magnitude, by means of chemical substitutions operated on the bridges connecting the two magnetic centers. The level of detail provided by the magnetic exchange decomposition in terms of direct exchange, kinetic exchange, and core polarization puts forward the relative importance of the different bridges. At variance with the principal bridge for which chemical substitutions modify both the direct and the kinetic exchange contributions, modifications of the secondary bridge only affect the magnitude of the anti-ferromagnetic kinetic exchange mechanism, ultimately allowing for a direct control of the magnetic character of the modified compound.

Sampling the protonation states: the pH-dependent UV absorption spectrum of a polypeptide dyad.

When a chromophore interacts with several titratable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine-tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to help in the interpretation of the experimental tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that radical tryptophan probably contributes to the peptide spectrum, thanks to a UV-induced electron transfer from tyrosine to tryptophan, ultimately shedding light on the complex pH-dependent behavior of the peptide spectrum.

Mapping the ultrafast vibrational dynamics of all-trans and 13-cis retinal isomerization in Anabaena Sensory Rhodopsin.

Discrepancies in the isomerization dynamics and quantum yields of the trans and cis retinal protonated Schiff base is a well-known issue in the context of retinal photochemistry. Anabaena Sensory Rhodopsin (ASR) is a microbial retinal protein that comprises a retinal chromophore in two ground state (GS) conformations: all-trans, 15-anti (AT) and 13-cis, 15-syn (13C). In this study, we applied impulsive vibrational spectroscopic techniques (DFWM, pump-DFWM and pump-IVS) to ASR to shed more light on how the structural changes take place in the excited state within the same protein environment. Our findings point to distinct features in the ground state structural conformations as well as to drastically different evolutions in the excited state manifold. The ground state vibrational spectra show stronger Raman activity of the C14-H out-of-plane wag (at about 805 cm-1) for the 13C isomer than that for the AT isomer, which hints at a pre-distortion of 13C in the ground state. Evolution of the Raman frequency after interaction with the actinic pulse shows a blue-shift for the C[double bond, length as m-dash]C stretching and CH3 rocking mode for both isomers. For AT, however, the blue-shift is not instantaneous as observed for the 13C isomer, rather it takes more than 200 fs to reach the maximum frequency shift. This frequency blue-shift is rationalized by a decrease in the effective conjugation length during the isomerization reaction, which further confirms a slower formation of the twisted state for the AT isomer and corroborates the presence of a barrier in the excited state trajectory previously predicted by quantum chemical calculations.

pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin.

A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH. It relies on the existence of a protein structure, the prediction of titratable amino-acid pKa values and a very limited set of parameters. Applied to the case of the photochromic Anabaena sensory rhodopsin protein, the model succeeds in reproducing qualitatively the reported experimental data, confirming the importance of aspartic acid 217 in the observed blue shift in the λmax of ASR at neutral pH. It also suggests for the first time the role of two other amino acids, glutamic acid 36 at basic pH and aspartic acid 120 at acidic pH.

Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

Spin decontamination of broken-symmetry density functional theory calculations: deeper insight and new formulations.

This work re-examines the problem of the broken-symmetry Density-Functional Theory (DFT) solutions in diradical systems, in particular for the calculation of magnetic couplings. The Ms = 0 solution is not an eigenfunction of the S(2) spin operator and the evaluation of the singlet state energy requires a spin-decontamination. A popular approximation is provided by the so-called Yamaguchi formula, which operates using the expectation values of S(2) relative to both Ms = 1 and Ms =0 solutions. Referring to a previous decomposition of the magnetic coupling in terms of direct exchange, kinetic exchange and core polarization, it is shown that this expression will lead to unreliable values of the singlet-triplet energy gap when the spin polarization of the core orbitals becomes large. The here-proposed method of spin-decontamination is based on the Effective Hamiltonian Theory and uses the overlap between the two degenerate Ms = 0 solutions. An approximate and convenient formula, which uses the expectation values of S(2) of the Ms = 0 solutions before and after core polarization is proposed, which is free from the Yamaguchi's formula artefact, as illustrated on an organic diradical presenting a very high value of 〈S(2)〉 for the Ms = 0 solution, the antiferromagnetic coupling being due to the spin polarization mechanism.

Understanding bacterial bioluminescence: a theoretical study of the entire process, from reduced flavin to light emission.

Bacterial bioluminescence (BL) has been successfully applied in water-quality monitoring and in vivo imaging. The attention of researchers has been attracted for several decades, but the mechanism of bacterial BL is still largely unknown due to the complexity of the multistep reaction process. Debates mainly focus on three key questions: How is the bioluminophore produced? What is the exact chemical form of the bioluminophore? How does the protein environment affect the light emission? Using quantum mechanics (QM), combined QM and molecular mechanics (QM/MM) and molecular dynamic (MD) calculations in gas-phase, solvent and protein environments, the entire process of bacterial BL was investigated, from flavin reduction to light emission. This investigation revealed that: 1) the chemiluminescent decomposition of flavin peroxyhemiacetal does not occur through the intramolecular chemical initiated electron exchange luminescence (CIEEL) or the "dioxirane" mechanism, as suggested in the literature. Instead, the decomposition occurs according to the charge-transfer initiated luminescence (CTIL) mechanism for the thermolysis of dioxetanone. 2) The first excited state of 4a-hydroxy-4a,5-dihydroFMN (HFOH) was affirmed to be the bioluminophore of bacterial BL. This study provides details regarding the mechanism by which bacterial BL is produced and is helpful in understanding bacterial BL in general.

Theoretical study of the photochemical initiation in nitroxide-mediated photopolymerization.

Nitroxide-mediated photopolymerization (NMP(2)) is a promising novel route to initiate radical polymerization. In NMP(2), alkoxyamines bounded to a monomer are attached to a chromophore. Upon light absorption, the excitation energy is transferred from the chromophore to the alkoxyamine moiety, inducing the cleavage of the oxygen-carbon bond and thus initiating the polymerization. The NMP(2) mechanism depends strongly on several factors like the type of chromophore, the monomer, the connectivity pattern, etc. This complexity makes it difficult to design new NMP(2) initiators with increased polymerization efficiency and selectivity. In the present article, we characterize by means of quantum mechanical calculations the main steps of the NMP(2) initiation for alkoxyamines attached to aromatic ketones. We show how the excitation energy can be transferred from the chromophore to the alkoxyamine moiety, and present two easily computed parameters which can account for the selectivity of the O-C bond photocleaveage. Finally, using results obtained for a series of isomers, we give some rules that may help the design of more efficient NMP(2) initiators.