On the performance of composite schemes in determining equilibrium molecular structures.

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules. The ab initio calculations were performed using three tiers of composite chemical recipes. The current results show that as the overall rigor of calculation is increased, the semi-experimental and the ab initio numbers agree to within 0.0003 Å for all molecules in the test set. The composite approach based on correcting the potential energy surface (energy scheme) and the one based on correcting the geometry directly (geometry scheme) show excellent agreement with each other. This work represents a step toward development of efficient and highly accurate procedures for computing ab initio equilibrium structures.

Influence of fourth-order vibrational corrections on semi-experimental (reSE) structures of linear molecules.

Semi-experimental structures (reSE) are derived from experimental ground state rotational constants combined with theoretical vibrational corrections. They permit a meaningful comparison with equilibrium structures based on high-level ab initio calculations. Typically, the vibrational corrections are evaluated with second-order vibrational perturbation theory (VPT2). The amount of error introduced by this approximation is generally thought to be small; however, it has not been thoroughly quantified. Herein, we assess the accuracy of theoretical vibrational corrections by extending the treatment to fourth order (VPT4) for a series of small linear molecules. Typical corrections to bond distances are on the order of 10-5 Å. Larger corrections, nearly 0.0002 Å, are obtained to the bond lengths of NCCN and CNCN. A borderline case is CCCO, which will likely require variational computations for a satisfactory answer. Treatment of vibrational effects beyond VPT2 will thus be important when one wishes to know bond distances confidently to four decimal places (10-4 Å). Certain molecules with shallow bending potentials, e.g., HOC+, are not amenable to a VPT2 description and are not improved by VPT4.

Flexible switch matrix addressable electrode arrays with organic electrochemical transistor and pn diode technology.

Due to their effective ionic-to-electronic signal conversion and mechanical flexibility, organic neural implants hold considerable promise for biocompatible neural interfaces. Current approaches are, however, primarily limited to passive electrodes due to a lack of circuit components to realize complex active circuits at the front-end. Here, we introduce a p-n organic electrochemical diode using complementary p- and n-type conducting polymer films embedded in a 15-µm -diameter vertical stack. Leveraging the efficient motion of encapsulated cations inside this polymer stack and the opposite doping mechanisms of the constituent polymers, we demonstrate high current rectification ratios ([Formula: see text]) and fast switching speeds (230 µs). We integrate p-n organic electrochemical diodes with organic electrochemical transistors in the front-end pixel of a recording array. This configuration facilitates the access of organic electrochemical transistor output currents within a large network operating in the same electrolyte, while minimizing crosstalk from neighboring elements due to minimized reverse-biased leakage. Furthermore, we use these devices to fabricate time-division-multiplexed amplifier arrays. Lastly, we show that, when fabricated in a shank format, this technology enables the multiplexing of amplified local field potentials directly in the active recording pixel (26-µm diameter) in a minimally invasive form factor with shank cross-sectional dimensions of only 50×8 [Formula: see text].

Direct Probes of π-Delocalization in Prototypical Resonance-Stabilized Radicals: Hyperfine-Resolved Microwave Spectroscopy of Isotopic Propargyl and Cyanomethyl.

Delocalization of the unpaired electron in π-conjugated radicals has profound implications for their chemistry, but direct and quantitative characterization of this electronic structure in isolated molecules remains challenging. We apply hyperfine-resolved microwave rotational spectroscopy to rigorously probe π-delocalization in propargyl, CH2CCH, a prototypical resonance-stabilized radical and key reactive intermediate. Using the spectroscopic constants derived from the high-resolution cavity Fourier transform microwave measurements of an exhaustive set of 13C- and 2H-substituted isotopologues, together with high-level ab initio calculations of zero-point vibrational effects, we derive its precise semiexperimental equilibrium geometry and quantitatively characterize the spatial distribution of its unpaired electron. Our results highlight the importance of considering both spin-polarization and orbital-following contributions when interpreting the isotropic hyperfine coupling constants of π radicals. These physical insights are strengthened by a parallel analysis of the isoelectronic species cyanomethyl, CH2CN, using new 13C measurements also reported in this work. A detailed comparison of the structure and electronic properties of propargyl, cyanomethyl, and other closely related species allows us to correlate trends in their chemical bonding and electronic structure with critical changes in their reactivity and thermochemistry.

Polymer Modeling Reveals Interplay between Physical Properties of Chromosomal DNA and the Size and Distribution of Condensin-Based Chromatin Loops.

Transient DNA loops occur throughout the genome due to thermal fluctuations of DNA and the function of SMC complex proteins such as condensin and cohesin. Transient crosslinking within and between chromosomes and loop extrusion by SMCs have profound effects on high-order chromatin organization and exhibit specificity in cell type, cell cycle stage, and cellular environment. SMC complexes anchor one end to DNA with the other extending some distance and retracting to form a loop. How cells regulate loop sizes and how loops distribute along chromatin are emerging questions. To understand loop size regulation, we employed bead-spring polymer chain models of chromatin and the activity of an SMC complex on chromatin. Our study shows that (1) the stiffness of the chromatin polymer chain, (2) the tensile stiffness of chromatin crosslinking complexes such as condensin, and (3) the strength of the internal or external tethering of chromatin chains cooperatively dictate the loop size distribution and compaction volume of induced chromatin domains. When strong DNA tethers are invoked, loop size distributions are tuned by condensin stiffness. When DNA tethers are released, loop size distributions are tuned by chromatin stiffness. In this three-way interaction, the presence and strength of tethering unexpectedly dictates chromatin conformation within a topological domain.

Relation Between Bond Angle and Carbon-Oxygen Stretching Frequencies in CO2-Containing Compounds.

The symmetric (νs) and antisymmetric (νas) O-C-O stretching modes of CO2-containing compounds encode structural information that can be difficult to decipher, due to the sensitivity of these spectral features to small shifts in charge distribution and structure, as well as the anharmonicities of these two vibrational modes. In this work, we discuss the relation between the frequency of these modes and the geometry of the O-C-O group, showing that the splitting between νs and νas (Δνas-s = νas - νs) can be predicted based only on the O-C-O bond angle obtained from quantum chemical calculations with reasonable accuracy (±46 cm-1, R2 = 0.994). The relationship is shown to hold for the infrared spectra of a variety of CO2-containing molecules measured in vacuo. The origins of this model are discussed in the framework of elementary mode analysis.

Methanediol from cloud-processed formaldehyde is only a minor source of atmospheric formic acid.

Atmospheric formic acid is severely underpredicted by models. A recent study proposed that this discrepancy can be resolved by abundant formic acid production from the reaction (1) between hydroxyl radical and methanediol derived from in-cloud formaldehyde processing and provided a chamber-experiment-derived rate constant, k1 = 7.5 × 10-12 cm3 s-1. High-level accuracy coupled cluster calculations in combination with E,J-resolved two-dimensional master equation analyses yield k1 = (2.4 ± 0.5) × 10-12 cm3 s-1 for relevant atmospheric conditions (T = 260-310 K and P = 0-1 atm). We attribute this significant discrepancy to HCOOH formation from other molecules in the chamber experiments. More importantly, we show that reversible aqueous processes result indirectly in the equilibration on a 10 min. time scale of the gas-phase reaction [Formula: see text] (2) with a HOCH2OH to HCHO ratio of only ca. 2%. Although HOCH2OH outgassing upon cloud evaporation typically increases this ratio by a factor of 1.5-5, as determined by numerical simulations, its in-cloud reprocessing is shown using a global model to strongly limit the gas-phase sink and the resulting production of formic acid. Based on the combined findings in this work, we derive a range of 1.2-8.5 Tg/y for the global HCOOH production from cloud-derived HOCH2OH reacting with OH. The best estimate, 3.3 Tg/y, is about 30 times less than recently reported. The theoretical equilibrium constant Keq (2) determined in this work also allows us to estimate the Henry's law constant of methanediol (8.1 × 105 M atm-1 at 280 K).

Precise Equilibrium Structure of Benzene.

Recent advances in gas-phase structure determination afford outstanding agreement between the CCSD(T)/cc-pCVTZ-corrected semi-experimental (reSE) equilibrium structures and their corresponding best theoretical estimates (BTEs) of the equilibrium structures (re) based upon corrections to the CCSD(T)/cc-pCV5Z geometries for the aromatic heterocycles pyrimidine and pyridazine. Herein, that same analysis is extended to the fundamental aromatic molecule benzene, using published experimental spectroscopic data for a total of 11 available isotopologues. The incorporation of rotational constants from all of these isotopologues and CCSD(T) corrections to address the impacts of both the vibration-rotation interaction and electron-mass distribution results in a highly precise and accurate reSE structure. The CCSD(T)/cc-pCV5Z optimized geometry has been further corrected to address a finite basis set, untreated electron correlation, relativistic effects, and a breakdown of the Born-Oppenheimer approximation. This analysis achieves outstanding agreement between the re (BTE) and reSE structural parameters of benzene to a highly satisfying level (0.0001 Å), an agreement that surpasses our recently published structures of the aforementioned nitrogen-substituted benzene analogues. The D6h geometry of benzene is now known to an unprecedented precision: RC-C = 1.3913 (1) Å and RC-H = 1.0809 (1) Å. The mutual agreement between theory and experiment presented in this work validates both, substantially resolving all discrepancies between the reSE and theoretical re structures available in the literature.

Photoelectron Velocity Map Imaging Spectroscopy of the Beryllium Trimer and Tetramer.

Computational studies of small beryllium clusters (BeN) predict dramatic, nonmonotonic changes in the bonding mechanisms and per-atom cohesion energies with increasing N. To date, experimental tests of these quantum chemistry models are lacking for all but the Be2 molecule. In the present study, we report spectroscopic data for Be3 and Be4 obtained via anion photodetachment spectroscopy. The trimer is predicted to have D3h symmetric equilibrium structures for both the neutral molecule and the anion. Photodetachment spectra reveal transitions that originate from the X2A2″ ground state and the 12A1' electronically excited state. The state symmetries were assigned on the basis of anisotropic photoelectron angular distributions. The neutral and anionic forms of Be4 are predicted to be tetrahedral. Franck-Condon diagonal photodetachment was observed with a photoelectron angular distribution consistent with the expected Be4-X2A1 → Be4X1A1 transition. The electron affinities of Be3 and Be4 were determined to be 11363 ± 60 and 13052 ± 50 cm-1, respectively.

Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability.

Centromere (CEN) identity is specified epigenetically by specialized nucleosomes containing evolutionarily conserved CEN-specific histone H3 variant CENP-A (Cse4 in Saccharomyces cerevisiae, CENP-A in humans), which is essential for faithful chromosome segregation. However, the epigenetic mechanisms that regulate Cse4 function have not been fully defined. In this study, we show that cell cycle-dependent methylation of Cse4-R37 regulates kinetochore function and high-fidelity chromosome segregation. We generated a custom antibody that specifically recognizes methylated Cse4-R37 and showed that methylation of Cse4 is cell cycle regulated with maximum levels of methylated Cse4-R37 and its enrichment at the CEN chromatin occur in the mitotic cells. Methyl-mimic cse4-R37F mutant exhibits synthetic lethality with kinetochore mutants, reduced levels of CEN-associated kinetochore proteins and chromosome instability (CIN), suggesting that mimicking the methylation of Cse4-R37 throughout the cell cycle is detrimental to faithful chromosome segregation. Our results showed that SPOUT methyltransferase Upa1 contributes to methylation of Cse4-R37 and overexpression of UPA1 leads to CIN phenotype. In summary, our studies have defined a role for cell cycle-regulated methylation of Cse4 in high-fidelity chromosome segregation and highlight an important role of epigenetic modifications such as methylation of kinetochore proteins in preventing CIN, an important hallmark of human cancers.

Pharyngeal Co-Infections with Monkeypox Virus and Group A Streptococcus, United States, 2022.

We report 2 cases of pharyngeal monkeypox virus and group A Streptococcus co-infection in the United States. No rash was observed when pharyngitis symptoms began. One patient required intubation before mpox was diagnosed. Healthcare providers should be aware of oropharyngeal mpox manifestations and possible co-infections; early treatment might prevent serious complications.

Improved semi-experimental equilibrium structure and high-level theoretical structures of ketene.

The millimeter-wave rotational spectrum of ketene (H2C=C=O) has been collected and analyzed from 130 to 750 GHz, providing highly precise spectroscopic constants from a sextic, S-reduced Hamiltonian in the Ir representation. The chemical synthesis of deuteriated samples allowed spectroscopic measurements of five previously unstudied ketene isotopologues. Combined with previous work, these data provide a new, highly precise, and accurate semi-experimental (reSE) structure for ketene from 32 independent moments of inertia. This reSE structure was determined with the experimental rotational constants of each available isotopologue, together with computed vibration-rotation interaction and electron-mass distribution corrections from coupled-cluster calculations with single, double, and perturbative triple excitations [CCSD(T)/cc-pCVTZ]. The 2σ uncertainties of the reSE parameters are ≤0.0007 Å and 0.014° for the bond distances and angle, respectively. Only S-reduced spectroscopic constants were used in the structure determination due to a breakdown in the A-reduction of the Hamiltonian for the highly prolate ketene species. All four reSE structural parameters agree with the "best theoretical estimate" (BTE) values, which are derived from a high-level computed re structure [CCSD(T)/cc-pCV6Z] with corrections for the use of a finite basis set, the incomplete treatment of electron correlation, relativistic effects, and the diagonal Born-Oppenheimer breakdown. In each case, the computed value of the geometric parameter lies within the statistical experimental uncertainty (2σ) of the corresponding semi-experimental coordinate. The discrepancies between the BTE structure and the reSE structure are 0.0003, 0.0000, and 0.0004 Å for rC-C, rC-H, and rC-O, respectively, and 0.009° for θC-C-H.

Benchmarking Aspects of Ab Initio Fragment Models for Accurate Excimer Potential Energy Surfaces.

While Coupled-Cluster methods have been proven to provide an accurate description of excited electronic states, the scaling of the computational costs with the system size limits the degree for which these methods can be applied. In this work different aspects of fragment-based approaches are studied on noncovalently bound molecular complexes with interacting chromophores of the fragments, such as π-stacked nucleobases. The interaction of the fragments is considered at two distinct steps. First, the states localized on the fragments are described in the presence of the other fragment(s); for this we test two approaches. One method is founded on QM/MM principles, only including the electrostatic interaction between the fragments in the electronic structure calculation with Pauli repulsion and dispersion effects added separately. The other model, a Projection-based Embedding (PbE) using the Huzinaga equation, includes both electrostatic and Pauli repulsion and only needs to be augmented by dispersion interactions. In both schemes the extended Effective Fragment Potential (EFP2) method of Gordon et al. was found to provide an adequate correction for the missing terms. In the second step, the interaction of the localized chromophores is modeled for a proper description of the excitonic coupling. Here the inclusion of purely electrostatic contributions appears to be sufficient: it is found that the Coulomb part of the coupling provides accurate splitting of the energies of interacting chromophores that are separated by more than 4 Å.

Calculated and Empirical Values of Vibronic Transition Dipole Moments of Reactive Chemical Intermediates for Determination of Concentrations.

Absorption spectroscopy has long been known as a technique for making molecular concentration measurements and has received enhanced visibility in recent years with the advent of new techniques, like cavity ring-down spectroscopy, that have increased its sensitivity. To apply the method, it is necessary to have a known molecular absorption cross section for the species of interest, which typically is obtained by measurements of a standard sample of known concentration. However, this method fails if the species is highly reactive, and indirect means for attaining the cross section must be employed. The HO2 and alkyl peroxy radicals are examples of reactive species for which absorption cross sections have been reported. This work explores and describes for these peroxy radicals the details of an alternative approach for obtaining these cross sections using quantum chemistry methods for the calculation of the transition dipole moment upon whose square the cross section depends. Likewise, details are given for obtaining the transition moment from the experimentally measured cross sections of individual rovibronic lines in the near-IR Ã-X̃ electronic spectrum of HO2 and the peaks of the rotational contours in the corresponding electronic transitions for the alkyl (methyl, ethyl, and acetyl) peroxy radicals. In the case of the alkyl peroxy radicals, good agreement for the transition moments, ≈20%, is found between the two methods. However, rather surprisingly, the agreement is significantly poorer, ≈40%, for the HO2 radical. Possible reasons for this disagreement are discussed.

Vibrationally excited states of 1H- and 2H-1,2,3-triazole isotopologues analyzed by millimeter-wave and high-resolution infrared spectroscopy with approximate state-specific quartic distortion constants.

In this work, we present the spectral analysis of 1H- and 2H-1,2,3-triazole vibrationally excited states alongside provisional and practical computational predictions of the excited-state quartic centrifugal distortion constants. The low-energy fundamental vibrational states of 1H-1,2,3-triazole and five of its deuteriated isotopologues ([1-2H]-, [4-2H]-, [5-2H]-, [4,5-2H]-, and [1,4,5-2H]-1H-1,2,3-triazole), as well as those of 2H-1,2,3-triazole and five of its deuteriated isotopologues ([2-2H]-, [4-2H]-, [2,4-2H]-, [4,5-2H]-, and [2,4,5-2H]-2H-1,2,3-triazole), are studied using millimeter-wave spectroscopy in the 130-375 GHz frequency region. The normal and [2-2H]-isotopologues of 2H-1,2,3-triazole are also analyzed using high-resolution infrared spectroscopy, determining the precise energies of three of their low-energy fundamental states. The resulting spectroscopic constants for each of the vibrationally excited states are reported for the first time. Coupled-cluster vibration-rotation interaction constants are compared with each of their experimentally determined values, often showing agreement within 500 kHz. Newly available coupled-cluster predictions of the excited-state quartic centrifugal distortion constants based on fourth-order vibrational perturbation theory are benchmarked using a large number of the 1,2,3-triazole tautomer isotopologues and vibrationally excited states studied.

Rotamers of Methanediol: Composite Ab Initio Predictions of Structures, Frequencies, and Rovibrational Constants.

Geminal diols are known to be important intermediates in atmospheric ozonolysis and the aerosol cycle. Recently, the simplest member of this class, methanediol, was interrogated in the gas phase with infrared spectroscopy. To aid in future spectroscopic investigations of methanediol, including in the interstellar medium, we report fundamental frequencies and rovibrational constants for the two rotamers of this molecule using ab initio composite methods along with vibrational perturbation theory. Sensitivity of the predictions to the level of theory and the treatment of anharmonic resonances are carefully assessed. The OH stretching harmonic frequencies of both rotamers are particularly sensitive to the level of theory. The CH stretches of the Cs rotamer are sensitive to the treatment of anharmonic resonances with VPT2-based effective Hamiltonian models. Equilibrium bond distances and harmonic frequencies are converged conservatively to within 0.0005 Å and 3 cm-1, respectively. The effect of tunneling on the rotational constants is investigated with a 2D variational calculation, based on a relaxed hydroxyl torsional potential energy surface. Tunneling is found to be negligible in the lower energy C2 rotamer but should modify the rotational constants of the Cs rotamer on the order of MHz, giving rise to rotational line splittings of the same order. The rovibrational constants of the Cs rotamer are dominated by hydroxyl torsional effects, and here we see evidence for the breakdown of vibrational perturbation theory.

Connections between the accuracy of rotational constants and equilibrium molecular structures.

Rotational spectroscopy is the technique of choice for investigating molecular structures in the gas phase. Indeed, rotational constants are strongly connected to the geometry of the molecular system under consideration. Therefore, they are powerful tools for assessing the accuracy that quantum chemical approaches can reach in structural determinations. In this review article, it is shown how it is possible to measure the accuracy of a computed equilibrium geometry based on the comparison of rotational constants. But, it is also addressed what accuracy is required by computations for providing molecular structures and thus rotational constants that are useful to experiment. Quantum chemical methodologies for obtaining the "0.1% accuracy" for rotational constants are reviewed for systems ranging in size from small molecules to small polycyclic aromatic hydrocarbons. This accuracy for systems containing two dozen or so atoms opens the way towards future applications such as the accurate characterization of non-covalent interactions, which play a key role in several biological and technological processes.

Sub 20 cm-1 computational prediction of the CH bond energy - a case of systematic error in computational thermochemistry.

The bond dissociation energy of methylidyne, D0(CH), is studied using an improved version of the High-Accuracy Extrapolated ab initio Thermochemistry (HEAT) approach as well as the Feller-Peterson-Dixon (FPD) model chemistry. These calculations, which include basis sets up to nonuple (aug-cc-pCV9Z) quality, are expected to be capable of providing results substantially more accurate than the ca. 1 kJ mol-1 level that is characteristic of standard high-accuracy protocols for computational thermochemistry. The calculated 0 K CH bond energy (27 954 ± 15 cm-1 for HEAT and 27 956 ± 15 cm-1 for FPD), along with equivalent treatments of the CH ionization energy and the CH+ dissociation energy (85 829 ± 15 cm-1 and 32 946 ± 15 cm-1, respectively), were compared to the existing benchmarks from Active Thermochemical Tables (ATcT), uncovering an unexpected difference for D0(CH). This has prompted a detailed reexamination of the provenance of the corresponding ATcT benchmark, allowing the discovery and subsequent correction of a systematic error present in several published high-level calculations, ultimately yielding an amended ATcT benchmark for D0(CH). Finally, the current theoretical results were added to the ATcT Thermochemical Network, producing refined ATcT estimates of 27 957.3 ± 6.0 cm-1 for D0(CH), 32 946.7 ± 0.6 cm-1 for D0(CH+), and 85 831.0 ± 6.0 cm-1 for IE(CH).

Pure Rotational Spectroscopy of the CH2CN Radical Extended to the Sub-Millimeter Wave Spectral Region.

We present a thorough pure rotational investigation of the CH2CN radical in its ground vibrational state. Our measurements cover the millimeter and sub-millimeter wave spectral regions (79-860 GHz) using a W-band chirped-pulse instrument and a frequency multiplication chain-based spectrometer. The radical was produced in a flow cell at room temperature by H abstraction from acetonitrile using atomic fluorine. The newly recorded transitions of CH2CN (involving N″ and Ka″ up to 42 and 8, respectively) were combined with the literature data, leading to a refinement of the spectroscopic parameters of the species using a Watson S-reduced Hamiltonian. In particular, the A rotational constant and K-dependent parameters are significantly better determined than in previous studies. The present model, which reproduces all experimental transitions to their experimental accuracy, allows for confident searches for the radical in cold to warm environments of the interstellar medium.