P490 Fatal secondary fungemia due to Trichosporon asahii onychomycosis in a diabetic patient

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM

 

Objectives

We describe a fatal case of trichosporonosis caused by Trichosporon asahii. The aim was to molecularly characterize the T. asahii strains from blood and foot tissue samples to investigate their genetic relatedness.

Case

An 85-year-old morbidly obese female with a prior cerebrovascular accident, hypertension, and diabetes mellitus was admitted to a peripheral hospital with type II respiratory failure, metabolic acidosis, and chronic anemia. Three weeks post-hospitalization the patient remained febrile, physical examination showed that the patient had paronychia, nail pigmentation, subungual onychomycosis, and a diabetic foot ulcer. Blood culture, as well as nail and ulcer samples, became positive for Trichosporon yeasts.

Methods

Trichosporon yeasts were subjected to molecular identification by sequencing the intergenic spacer (IGS1) region. Minimal inhibitory concentrations (MICs) were determined by the EUCAST microdilution method. Long-read nanopore sequencing was performed for the three clinical strains, the type-strain of T. asahii (CBS2479), and two IGS-genotype 7 strains (CBS2936, CBS7632) using the native barcoding kit v12 (SQK-LSK112; Oxford Nanopore Technologies). Raw data were basecalled with Guppy v6, Flye v2.9 was used to de novo assemble the genome of CBS2479, this was used as a reference for variant calling using the genomic reads of all strains.

Results

The three clinical strains were found to belong to the rare IGS-genotype 7 and had similar MICs for amphotericin B (4 µg/ml), 5-fluorocytosine and fluconazole (2 µg/ml), voriconazole (≤ 0.015 µg/ml), posaconazole (0.0625 µg/ml), itraconazole (0.125 µg/ml), caspofungin (8 µg/ml), anidulafungin and micafungin (> 16 µg/ml). Strains from the ulcer and nail were genetically very closely related with 10 836 SNPs differences, the blood-derived strain differed more from these two strains with 94 729 SNPs and 94 913 SNPs, respectively. Strains CBS2936 and CBS7632 were only distantly related to CBS2479 with 328 221, and 436 060 SNPs, respectively.

Conclusion

The T. Asahii IGS-genotype 7 strain causing fatal fungemia was genetically nearly identical to that obtained from nail and foot ulcers, making it highly likely that this was the port d'entrée for T. asahii.

Localization and Delocalization in Solids from Electron Distribution Functions

The extent of electron localization and delocalization in molecular and condensed phases has been the subject of intense scrutiny over the years. In Chemistry, where real, instead of momentum space viewpoints are many times closer to intuition, a plethora of localization descriptors exist, including a family of indices invariant under orbital transformations that rely only on an underlying partition of the physical space into meaningful regions. These localization and delocalization indices measure the fluctuation of the electron population contained in such domains, and have been rigorously related to the insulating or conductive character of extended systems. Knowledge of the full electron population probability distribution function is also available in molecules, where it has provided many meaningful results as well as uncovered exotic interaction regimes in excited states. Electron distribution functions (EDFs), which can be seen as real space analogs of Pauling resonance structures, are now reported in periodic systems. In agreement with what is known in finite systems, ionic compounds display narrow EDFs that get wider as covalency sets in. Contrarily to conventional wisdom, most electrons delocalize over their nearest neighbors, even in quasi electron-gas metals like sodium, and it is only in the decay rate of the probability distribution where conductors and insulators can be distinguished.

Questioning the orbital picture of magnetic spin coupling: a real space alternative

The prevailing magnetic spin coupling paradigm is based on a one-electron picture, and is therefore orbital dependent and unsatisfactory from a physical point of view. We examine it under a truly invariant real space perspective, focusing on the role of electron delocalization. We show that this view, compatible with orbital thinking, overcomes its limitations. By examining simple model systems we show that it is electron delocalization that drives any singlet-triplet gap, and that delocalization and ionic mixing are two sides of the same reality. It is in the end delocalization, fostered or hindered by the specific structure of a system, that lies behind its preferred magnetic coupling mode. In the case of superexchange-mediated coupling through atomic bridges, we also point out the non-essential role of the bridge's electrons in setting up singlet-triplet preferences. We show that the use of real space thinking allows for tuning singlet-triplet gaps using knobs that are not easily grasped from the orbital standpoint, opening new avenues in the design and control of molecular magnets.

Local spin and open quantum systems: clarifying misconceptions, unifying approaches

The theory of open quantum systems (OQSs) is applied to partition the squared spin operator into fragment (local spin) and interfragment (spin-coupling) contributions in a molecular system.

Cardiac arrest after a cerebral gas embolism. Case report

Cerebral arterial gas embolism is a serious and often iatrogenic fatal event associated with invasive procedures. It is a possible cause of a cardiac arrest and the diagnosis is challenging. We report a case of a cardiac arrest after a cerebral arterial gas embolism, in a 63-year-old male subjected to a Computed Tomography-guided Transthoracic Needle Aspiration Biopsy, which was successfully managed with hyperbaric oxygen therapy.

Electronegativity equalization: taming an old problem with new tools

Electronegativity equalization is examined after understanding an atom-in-a-molecule as an open quantum system, characterized by a variable fluctuating number of electrons whose average is set through charge-constrained electronic structure calculations. It is shown that actual results in toy systems can be easily modeled through electron distribution functions, and that by doing so several conflicting interpretations converge onto a common formalism.

Reply to the ‘Comment on “Decoding real space bonding descriptors in valence bond language”’ by S. Shaik, P. Hiberty and D. Danovich, Phys. Chem. Chem. Phys., 2019, 21, DOI: 10.1039/C8CP07225F

The concerns posed by S. Shaik, P. Hiberty and D. Danovich regarding the mapping between quantum chemical topology (QCT) and valence bond (VB) concepts are discussed and clarified. We stress that we do not redefine the VB concept of the resonance structure but that we compare it with its QCT equivalent in real space.

Electron-pair bonding in real space. Is the charge-shift family supported?

Charge-shift bonding (CSB) has been introduced as a distinct third family of electron-pair links that adds to the covalent and ionic tradition.

Decoding real space bonding descriptors in valence bond language

Real space bonding descriptors are orbital invariant indices that can be obtained independently of the theoretical framework used to compute a given wavefunction. Here we show how to use them to read in real space some widely used concepts in Valence Bond (VB) theory, such as ionic/covalent characters or covalent-ionic resonance energies. All of these are essential ingredients used when building VB chemical insight. Electron number distribution functions are employed to directly map ionic and covalent weights with real space delocalization indices. We show that covalency, understood as delocalization, emerges in position space from the fluctuation of electron populations. This is mapped in VB to covalent-ionic resonance. The reasons why this is not so in the standard language of non-orthogonal VB are examined. A simple real space ionic character index that maintains the essence of its VB equivalent is defined and examined in simple model systems. The conclusions of this work ease travelling among the sometimes conflicting molecular orbital, real space, and valence bond interpretations in chemical bonding theory.

From quantum fragments to Lewis structures: electron counting in position space

From quantum atoms to electron counting the rs-AdNCP strategy: a Lewis structure through (nc,2e) functions.

Real space bond orders are energetic descriptors

Orbital invariant position space techniques are used to show a theoretical link between the conventional concept of bond order and the energetics of chemical interactions.

Decay rate of real space delocalization measures: a comparison between analytical and test systems

We examine in this contribution the possible relation between the spatial decay rate of real space delocalization measures and the insulating- or metallic-like character of molecular and extended systems. We first show that in simple one-electron models, like the Hückel or tight binding approximations, delocalization indices (DIs) are intimately linked to the first-order reduced density matrix (1RDM), whose decay rate is known to be exponential in gapped systems and algebraic in gapless ones. DIs are shown to behave equivalently, with wild oscillations in gapless 1D, 2D and 3D models that do only persist in one-dimensional real cases, as computed at the Hartree-Fock or Kohn-Sham levels. Oscillations are shown to be directly related to Pauling resonant structures and chemical mesomerism. DIs in insulating-like moieties decay extremely fast. We propose that examining the decay of DIs along different directions in real materials may be used to detect facile and non-facile conductivity channels.

Chemical Interactions and Spin Structure in (O2)4: Implications for the ε-O2 Phase

The chemical interactions and spin structure of (O2)4 in its ground singlet state are analyzed by means of Quantum Chemical Topology descriptors. The energetic contributions of the Interacting Quantum Atoms approach are used to obtain information about the class of interactions displayed along the dissociation path of (O2)4. The exchange-correlation contribution to the binding energy is non-negligible for the O2-O2 interactions at intermolecular distances close to those found for the pressure induced ε phase of solid (O2) and this strengthening of the intermolecular bonding is built up from a simultaneous weakening of the intramolecular bond. This result is of interest in connection with the observed softening of the IR vibron frequency in the lower pressure range of the ε phase. The spin structure in the real space along the dissociation process is interpreted with the help of the so-called electron number distribution functions. At large distances, the four triplet O2 molecules are arranged in a way consistent with an antiferromagnetic structure, whereas at short distances, a significant spin redistribution is driven by the exchange process and it involves a propensity toward a null magnetic moment per molecule. Such probability behavior can be related with the magnetic evolution of solid oxygen across the δ → ε phase transition. Additional calculations of (O2)4 excited states support the conclusion that the relative stabilization and magnetic features of the ground singlet state are due to the onset of the new intermolecular bonds, and not to an exclusive modification of the electronic character within the O2 molecules.

Domain-averaged exchange-correlation energies as a physical underpinning for chemical graphs

A novel solution to the problem of assigning a molecular graph to a collection of nuclei (i.e. how to draw a molecular structure) is presented. Molecules are universally understood as a set of nuclei linked by bonds, but establishing which nuclei are bonded and which are not is still an empirical matter. Our approach borrows techniques from quantum chemical topology, which showed for the first time the construction of chemical graphs from wave functions, shifting the focus on energetics. This new focus resolves issues surrounding previous topological analyses, in which domain-averaged exchange-correlation energies (V(xc)), quantities defined in real space between each possible atom pair, hold the key. Exponential decay of V(xc) in non-metallic systems as the intercenter distance increases guarantees a well-defined hierarchy for all possible V(xc) values in a molecule. Herein, we show that extracting the set of atom pairs that display the largest V(xc) values in the hierarchy is equivalent to retrieving the molecular graph itself. Notably, domain-averaged exchange-correlation energies are transferable, and they can be used to calculate bond strengths. Fine-grained details resulted to be related to simple stereoelectronic effects. These ideas are demonstrated in a set of simple pilot molecules.

Performance of the density matrix functional theory in the quantum theory of atoms in molecules

The generalization to arbitrary molecular geometries of the energetic partitioning provided by the atomic virial theorem of the quantum theory of atoms in molecules (QTAIM) leads to an exact and chemically intuitive energy partitioning scheme, the interacting quantum atoms (IQA) approach, that depends on the availability of second-order reduced density matrices (2-RDMs). This work explores the performance of this approach in particular and of the QTAIM in general with approximate 2-RDMs obtained from the density matrix functional theory (DMFT), which rests on the natural expansion (natural orbitals and their corresponding occupation numbers) of the first-order reduced density matrix (1-RDM). A number of these functionals have been implemented in the promolden code and used to perform QTAIM and IQA analyses on several representative molecules and model chemical reactions. Total energies, covalent intra- and interbasin exchange-correlation interactions, as well as localization and delocalization indices have been determined with these functionals from 1-RDMs obtained at different levels of theory. Results are compared to the values computed from the exact 2-RDMs, whenever possible.

Vibrotactile amplitude discrimination capacity parallels magnitude changes in somatosensory cortex and follows Weber's Law

In this study, we investigated the changes in perceptual metrics of amplitude discrimination that were observed in ten healthy human subjects with increasing intensities of stimulation. The ability to perceive differences in vibrotactile amplitude changed systematically with increasing stimulus magnitude (i.e., followed Weber's Law) in a near linear fashion (R (2) = 0.9977), and the linear fit determined by the amplitude discrimination task predicted the subjects' detection thresholds. Additionally, the perceptual metrics correlated well with observations from a previously reported study in which measures of SI cortical activity in non-human primates (squirrel monkeys) evoked by different amplitudes of vibrotactile stimulation were obtained (Simons et al. in BMC Neurosci 6:43, 2005). Stimuli were delivered simultaneously to two different skin sites (D2 and D3), enabling a method for the relatively rapid acquisition of the data. Stability and robustness of the measure, its rapid acquisition, and its apparent relationship with responses previously observed in SI cortex, led to the conclusion that deviations from the baseline values observed in the obtained perceptual metric could provide a useful indicator of cerebral cortical health.

Global optimization of ionic Mg(n)F(2n) (n=1-30) clusters

The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of Mg(n)F(2n) (n=1-30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5 x 10(4) BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0 bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.

Electron number probability distributions for correlated wave functions

Efficient formulas for computing the probability of finding exactly an integer number of electrons in an arbitrarily chosen volume are only known for single-determinant wave functions [E. Cances et al., Theor. Chem. Acc. 111, 373 (2004)]. In this article, an algebraic method is presented that extends these formulas to the case of multideterminant wave functions and any number of disjoint volumes. The derived expressions are applied to compute the probabilities within the atomic domains derived from the space partitioning based on the quantum theory of atoms in molecules. Results for a series of test molecules are presented, paying particular attention to the effects of electron correlation and of some numerical approximations on the computed probabilities.

Chemical fragments in real space: definitions, properties, and energetic decompositions

The physical and chemical meaning of real space molecular fragments resulting from arbitrary partitions of the density is reviewed under a common unifying formalism. Both fuzzy (interpenetrating) and non-fuzzy (exhaustive) decompositions are treated on an equal basis. Density decompositions are consistently generalized to compatible density matrix partitions by using Li and Parr's ideas (Li and Parr J Chem Phys 1986, 84, 1704), and these are carried onto an energy partition. It is argued that the merits of a given decomposition should be judged against both the charge and the energetic image it provides. Atomic partitions are used to show how the interacting quantum atoms approach (IQA) allows us to cope with the most important energy cancellations of quantum chemistry. Binding results from a trade-off between atomic (or fragment) energy deformations with respect to a reference and interatomic (interfragment) interactions. Deformation energies are divided into charge transfer and redistribution terms and their relative roles are analyzed. A number of systems are compared against the fuzziness of different density decompositions. The results consistently show that fuzzy partitions tend to give low atomic net charges and enhanced covalency, while exhaustive partitions generate larger net charges and smaller covalencies, across a wide range of bonding regimes.

An electron number distribution view of chemical bonds in real space

Several key concepts of chemical bonding theory, such as electron pair sharing, polarity, charge transfer, multiple bonding, etc., are shown to be recovered from the statistical properties of multivariate electron number distribution functions. The latter are constructed from the real-space atomic partition provided by the quantum theory of atoms in molecules. We present the basic formalism and several exemplifying calculations.

Pauling Resonant Structures in Real Space through Electron Number Probability Distributions

A general hierarchy of the coarsed-grained electron probability distributions induced by exhaustive partitions of the physical space is presented. It is argued that when the space is partitioned into atomic regions the consideration of these distributions may provide a first step toward an orbital invariant treatment of resonant structures. We also show that, in this case, the total molecular energy and its components may be partitioned into structure contributions, providing a fruitful extension of the recently developed interacting quantum atoms approach (J. Chem. Theory Comput. 2005, 1, 1096). The above ideas are explored in the hydrogen molecule, where a complete statistical and energetic decomposition into covalent and ionic terms is presented.

Charge transfer, chemical potentials, and the nature of functional groups: answers from quantum chemical topology

We analyze the response of a quantum group within a molecule to charge transfer by using the interacting quantum atoms approach (IQA), an energy partitioning scheme within the quantum theory of atoms in molecules (QTAM). It is shown that this response lies at the core of the concept of the functional group. The manipulation of fractional electron populations is carried out by using distribution functions for the electron number within the quantum basins. Several test systems are studied to show that similar chemical potential groups are characterized by similar energetic behavior upon interaction with other groups. The origin of the empirical additivity rules for group energies in simple hydrocarbons is also investigated. It turns out to rest on the independent saturation of both the self-energies and the interaction energies of the groups as the size of the chain increases. We also show that our results are compatible with the standard group energies of the QTAM.

The nature of the hydrogen bond: A synthesis from the interacting quantum atoms picture

The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50 years old debate regarding the covalent/electrostatic nature of the hydrogen bond.

Binding Energies of First Row Diatomics in the Light of the Interacting Quantum Atoms Approach

Binding energies of first row diatomics are revisited within the interacting quantum atoms (IQA) approach. This is a formalism in chemical bonding theory based upon the quantum theory of atoms in molecules. It is characterized by the preservation of the energetic identity of atoms within molecules. Quantum mechanically computed binding energies are recovered in IQA as a sum of small atomic deformation energies and large pairwise interaction terms. We show how this partition responds faithfully to chemical intuition, and how the different evolution of deformations and interactions accounts in a unified manner for the subtle variations of the binding energy of these molecules.

Two-electron integrations in the quantum theory of atoms in molecules

A method to compute two-electron integrals over arbitrary regions of space is introduced and particularized to the basins appearing in the quantum theory of atoms in molecules. The procedure generalizes the conventional multipolar approach to account for overlapping densities. We show that the approach is always convergent and computationally efficient, scaling as N(4) in the worst, two-center case. Several numerical results supporting our claims are also presented.

First Principles Study of Neutral and Anionic (Medium-Size) Aluminum Nitride Clusters: AlnNn,n= 7−16

We report the results of a theoretical study of AlnNn (n=7-16) clusters that is based on density functional theory. We will focus on the evolution of structural and electronic properties with the cluster size in the stoichiometric AlN clusters considered. The results reveal that the structural and electronic properties tend to evolve toward their respective bulk limits. The rate of evolution is, however, slow due to the hollow globular shape exhibited by the clusters, which introduces large surface effects that dominate the properties studied. We will also discuss the changes induced upon addition of an extra electron to the respective neutral clusters.