The verification of delta SCF and Slater's transition state theory for the calculation of core ionization energy.

The core ionization energies of second- and third-period elements of the molecules C2 H5 NO2 , SiF4 , Si(CH3 )4 , PF3 , POF3 , PSF3 , CS2 , OCS, SO2 , SO2 F2 , CH3 Cl, CFCl3 , SF5 Cl, and Cl3 PS are calculated by using Hartree-Fock (HF), and Kohn-Sham (KS) with BH&HLYP, B3LYP, and LC-BOP functionals. We used ΔSCF, Slater's transition state (STS), and two previously proposed shifted STS (1) and shifted STS (2) methods, which have been developed. The errors of ΔSCF and STS come mainly from the self-interaction errors (SIE) and can be corrected with a shifting scheme. In this study, we used the shifting parameters determined for each atom. The shifted STS (1) reproduces ΔSCF almost perfectly with mean absolute deviations (MAD) of 0.02 eV. While ΔSCF and STS vary significantly depending on the functional used, the variation of shifted STS (2) is small, and all shifted STS (2) values are close to the observed ones. The deviations of the shifted STS (2) from the experiment are 0.24 eV (BH&HLYP), 0.19 eV (B3LYP), and 0.23 eV (LC-BOP). These results further support the use of shifted STS methods for predicting the core ionization energies.

Single-cell dissection reveals the role of DNA damage response patterns in tumor microenvironment components contributing to colorectal cancer progression and immunotherapy.

Colorectal cancer (CRC) is one of the leading malignant cancers. DNA damage response (DDR), referring to the molecular process of DNA damage, is emerging as a promising field in targeted cancer therapy. However, the engagement of DDR in the remodeling of the tumor microenvironment is rarely studied. In this study, by sequential nonnegative matrix factorization (NMF) algorithm, pseudotime analysis, cell-cell interaction analysis, and SCENIC analysis, we have shown that DDR genes demonstrate various patterns among different cell types in CRC TME (tumor microenvironment), especially in epithelial cells, cancer-associated fibroblasts, CD8+ T cells, tumor-associated macrophages, which enhance the intensity of intercellular communication and transcription factor activation. Furthermore, based on the newly identified DDR-related TME signatures, cell subtypes including MNAT+CD8+T_cells-C5, POLR2E+Mac-C10, HMGB2+Epi-C4, HMGB1+Mac-C11, PER1+Mac-C5, PER1+CD8+T_cells-C1, POLR2A+Mac-C1, TDG+Epi-C5, TDG+CD8+T_cells-C8 are determined as critical prognostic factors for CRC patients and predictors of immune checkpoint blockade (ICB) therapy efficacy in two public CRC cohorts, TCGA-COAD and GSE39582. Our novel and systematic analysis on the level of the single-cell analysis has revealed the unique role of DDR in remodeling CRC TME for the first time, facilitating the prediction of prognosis and guidance of personalized ICB regimens in CRC.

Many-body Effects on Electronic Transport in Molecular Junctions: A Quantum Perspective.

This concept delves into quantum particle transport at the nanoscale, with a particular focus on how electrons move through molecular circuits. The thriving field of single molecular electronics benefits from the unique electrical and other properties of nanostructures. It concentrates on single molecular junctions that serve as bridges between electrodes. In this context, the electronic correlation-induced many-body effect gives rise to resonant states. These states, along with conductance, depend on electron spin. Thus, the field acts as a bridge between quantum and macroscopic worlds, unveiling unique behaviors of electrons. Additionally, external factors, such as magnetic fields and voltages, offer means to control the electron correlation in these junctions.

Sorting drug conformers in enzyme active sites: the XTB way.

In the present study, we have used the MEI196 set of interaction energies to investigate low-cost computational chemistry approaches for the calculation of binding between a molecule and its environment. Density functional theory (DFT) methods, when used with the vDZP basis set, yield good agreement with the reference energies. On the other hand, semi-empirical methods are less accurate as expected. By examining different groups of systems within MEI196 that contain species of a similar nature, we find that chemical similarity leads to cancellation of errors in the calculation of relative binding energies. Importantly, the semi-empirical method GFN1-xTB (XTB1) yields reasonable results for this purpose. We have thus further assessed the performance of XTB1 for calculating relative energies of docking poses of substrates in enzyme active sites represented by cluster models or within the ONIOM protocol. The results support the observations on error cancellation. This paves the way for the use of XTB1 in parts of large-scale virtual screening workflows to accelerate the drug discovery process.

Hydration Structure of 102No2+: A Density Functional Theory-Molecular Dynamics Study.

The hydration structure of No2+, the divalent cation of nobelium in water, was investigated by ab initio molecular dynamics (MD) simulations. First, a series of benchmark calculations were performed to validate the density functional theory (DFT) calculation methods for a molecule containing a No atom. The DFT-MD simulation of the hydration structure of No2+ was conducted after the MD method was validated by simulating the hydration structures of Ca2+ and Sr2+, whose behavior was previously reported to be similar to that of No2+. The model cluster containing M2+ (M = Ca, Sr, or No) and 32 water molecules was used for DFT-MD simulation. The results showed that the hydration distance of No2+ was intermediate between those of Ca2+ and Sr2+. This trend in the hydration distance is in good agreement with the elution position trend obtained in a previous radiochemical experiment. The calculated No-O bond lengths in the optimized structure of [No(H2O)8]2+ was 2.59 Å, while the average No-O bond length of [No(H2O)8]2+ in water by DFT-MD was 2.55 Å. This difference implies the importance of dynamic solvent effects, considering the second (and further) coordination sphere in the theoretical calculation of solution chemistry for superheavy elements.

Cluster-in-Cluster Approach for Computing MP2-Level Vibrational Infrared Spectra of Large Molecular Clusters.

Constructing the Hessian matrix (HM) for large molecules demands huge computational resources. Here, we report a cluster-in-cluster (CIC) procedure for efficiently evaluating HM and dipole derivatives for large molecular clusters by employing the second-order Møller-Plesset perturbation (MP2) theory. The highlight of the proposal is the separation of the estimations of Hartree-Fock (HF) and post-HF components. The parent cluster with n molecules is divided (virtually) into n subclusters centering each monomer and accommodating its near neighbors decided by a distance cutoff. The HF-level HM is obtained by doing full calculation (FC), while the correlation part is approximated by the respective subclusters. A software automating the procedure [followed by calculating infrared (IR) frequencies and intensities] is applied to deduce the IR spectrum for a variety of molecular clusters, particularly water clusters of various sizes, containing up to ∼2000 basis functions. The accuracy of the IR spectrum constructed using CIC is remarkable, with a substantial time advantage (with respect to its FC counterpart). The reduced computational resources and the tractability of the computations are other major benefits of the procedure.

Lectin-based phototherapy targeting cell surface glycans for pancreatic cancer.

Pancreatic ductal adenocarcinoma (PDAC) is resistant to current treatments but lectin-based therapy targeting cell surface glycans could be a promising new horizon. Here, we report a novel lectin-based phototherapy (Lec-PT) that combines the PDAC targeting ability of rBC2LCN lectin to a photoabsorber, IRDye700DX (rBC2-IR700), resulting in a novel and highly specific near-infrared, light-activated, anti-PDAC therapy. Lec-PT cytotoxicity was first verified in vitro with a human PDAC cell line, Capan-1, indicating that rBC2-IR700 is only cytotoxic upon cellular binding and exposure to near-infrared light. The therapeutic efficacy of Lec-PT was subsequently verified in vivo using cell lines and patient-derived, subcutaneous xenografting into nude mice. Significant accumulation of rBC2-IR700 occurs as early as 2 hours postintravenous administration while cytotoxicity is only achieved upon exposure to near-infrared light. Repeated treatments further slowed tumor growth. Lec-PT was also assessed for off-target toxicity in the orthotopic xenograft model. Shielding of intraperitoneal organs from near-infrared light minimized off-target toxicity. Using readily available components, Lec-PT specifically targeted pancreatic cancer with high reproducibility and on-target, inducible toxicity. Rapid clinical development of this method is promising as a new modality for treatment of pancreatic cancer.

Analytical quadrature method using recurrence formulas for two-electron integrals of frequency-dependent Breit interaction.

A recursive scheme was proposed to calculate two-electron integrals of frequency-dependent Breit interactions in electronic structure calculations using Gaussian basis functions. As shown in a previous study [R. Ahlrichs, Phys. Chem. Chem. Phys. 8 (2006) 3072-3077], the vertical recurrence relation for the two-electron integrals of the general two-body potential is valid. In addition, the authors have shown that the horizontal case is also valid. Explicit expressions for generalized molecular incomplete gamma function corresponding to the frequency-dependent Gaunt and gauge potentials were then derived, along with their asymptotic formulas. In addition, an implementation for computing the generalized molecular incomplete gamma function was proposed. Through numerical calculations, the shape of the curves of the generalized molecular incomplete gamma functions were found to vary significantly from that of the zero-energy case with the increase in the energy variable.

Realistic nuclear charge distribution model function for analytic nuclear attraction integrals in Gaussian basis functions.

In electronic structure theory, the charge distribution of a nucleus is usually approximated by point charge, Gaussian function, or homogeneously charged sphere, because they have an analytical nuclear attraction integral (NAI) formula. However, these functions do not always provide good approximations for nuclei with large mass number. The two-parameter Fermi (2pF) distribution and more realistic distributions describe well even nuclei with large mass number but do not have analytical NAI formulas. We propose a new function model called augmented Gaussian 12 (AG12), which has sufficient number of parameters and analytical NAI formulas. With the proposed fitting scheme, the AG12 charge distribution model optimally reproduces 2pF and the more realistic charge distributions. Moreover, AG12 fitted to 2pF model reproduces the energy difference of hydrogen-like ions well between the Gaussian distribution and 2pF models. Calculations using AG12 also suggested necessity to use more realistic nuclear charge distributions than 2pF.

Theoretical elucidation of the structure, bonding, and reactivity of the CaMn4Ox clusters in the whole Kok cycle for water oxidation embedded in the oxygen evolving center of photosystem II. New molecular and quantum insights into the mechanism of the O-O bond formation.

This paper reviews our historical developments of broken-symmetry (BS) and beyond BS methods that are applicable for theoretical investigations of metalloenzymes such as OEC in PSII. The BS hybrid DFT (HDFT) calculations starting from high-resolution (HR) XRD structure in the most stable S1 state have been performed to elucidate structure and bonding of whole possible intermediates of the CaMn4Ox cluster (1) in the Si (i = 0 ~ 4) states of the Kok cycle. The large-scale HDFT/MM computations starting from HR XRD have been performed to elucidate biomolecular system structures which are crucial for examination of possible water inlet and proton release pathways for water oxidation in OEC of PSII. DLPNO CCSD(T0) computations have been performed for elucidation of scope and reliability of relative energies among the intermediates by HDFT. These computations combined with EXAFS, XRD, XFEL, and EPR experimental results have elucidated the structure, bonding, and reactivity of the key intermediates, which are indispensable for understanding and explanation of the mechanism of water oxidation in OEC of PSII. Interplay between theory and experiments have elucidated important roles of four degrees of freedom, spin, charge, orbital, and nuclear motion for understanding and explanation of the chemical reactivity of 1 embedded in protein matrix, indicating the participations of the Ca(H2O)n ion and tyrosine(Yz)-O radical as a one-electron acceptor for the O-O bond formation. The Ca-assisted Yz-coupled O-O bond formation mechanisms for water oxidation are consistent with recent XES and very recent time-resolved SFX XFEL and FTIR results.

Triple modal treatment comprising with proton beam radiation, hyperthermia, and gemcitabine/nab-paclitaxel for locally advanced pancreatic cancer: a phase I/II study protocol (TT-LAP trial).

BACKGROUND: Locally advanced pancreatic ductal adenocarcinoma (PDAC), accounting for about 30% of PDAC patients, is difficult to cure by radical resection or systemic chemotherapy alone. A multidisciplinary strategy is required and our TT-LAP trial aims to evaluate whether triple-modal treatment with proton beam therapy (PBT), hyperthermia, and gemcitabine plus nab-paclitaxel is a safe and synergistically effective treatment for patients with locally advanced PDAC. METHODS: This trial is an interventional, open-label, non-randomized, single-center, single-arm phase I/II clinical trial organized and sponsored by the University of Tsukuba. Eligible patients who are diagnosed with locally advanced pancreatic cancer, including both borderline resectable (BR) and unresectable locally advanced (UR-LA) patients, and selected according to the inclusion and exclusion criteria will receive triple-modal treatment consisting of chemotherapy, hyperthermia, and proton beam radiation. Treatment induction will include 2 cycles of chemotherapy (gemcitabine plus nab-paclitaxel), proton beam therapy, and 6 total sessions of hyperthermia therapy. The initial 5 patients will move to phase II after adverse events are verified by a monitoring committee and safety is ensured. The primary endpoint is 2-year survival rate while secondary endpoints include adverse event rate, treatment completion rate, response rate, progression-free survival, overall survival, resection rate, pathologic response rate, and R0 (no pathologic cancer remnants) rate. The target sample size is set at 30 cases. DISCUSSION: The TT-LAP trial is the first to evaluate the safety and effectiveness (phases1/2) of triple-modal treatment comprised of proton beam therapy, hyperthermia, and gemcitabine/nab-paclitaxel for locally advanced pancreatic cancer. ETHICS AND DISSEMINATION: This protocol was approved by the Tsukuba University Clinical Research Review Board (reference number TCRB22-007). Results will be analyzed after study recruitment and follow-up are completed. Results will be presented at international meetings of interest in pancreatic cancer plus gastrointestinal, hepatobiliary, and pancreatic surgeries and published in peer-reviewed journals. TRIAL REGISTRATION: Japan Registry of Clinical Trials, jRCTs031220160. Registered 24 th June 2022, https://jrct.niph.go.jp/en-latest-detail/jRCTs031220160 .

Imaging of diffuse fibroepithelial polyps on surgical free flap in oral cancer patients: two case reports.

Fibroepithelial polyp (FEP) is a common benign tumor occurring in the skin and genitourinary tract, and there are no reports of multiple FEPs occurring on the myocutaneous flap. We report two cases of FEPs occurring diffusely on the skin tissue of the free anterolateral thigh flap after surgical reconstruction for oral squamous cell carcinoma. Clinically, multiple papillary nodules on the myocutaneous flap gradually increased. CT and MRI showed multiple papillary nodules on an enhanced layer covering the entire myocutaneous flap. PET/CT showed high uptake. One case was diagnosed with FEPs by surgery, the other by biopsy. The tumor-limited localization on the myocutaneous flap, characteristic morphology showing multiple papillary projection with an enhanced layer, and MRI signal showing patchy mild elevation of the apparent diffusion coefficient value may help in differential diagnosis from tumor recurrence or secondary carcinoma of the myocutaneous flap on diagnostic imaging.

Core-Level 2s and 2p Binding Energies of Third-Period Elements (P, S, and Cl) Calculated by Hartree-Fock and Kohn-Sham ΔSCF Theory.

In the present study, we investigate the use of the ΔSCF method and Slater's transition state (STS) theory to calculate the binding energies of the 2s and 2p electrons of third-period elements (P, S, and Cl). Both the Hartree-Fock (HF) and Kohn-Sham (KS) approximations are examined. The STS approximation performs well in reproducing the ΔSCF values. However, for the ΔSCF method itself, while the binding energy of the 2p electrons is accurately predicted, the results for 2s are fairly sensitive to the functional, exhibiting significant variations due to self-interaction errors (SIE). Nonetheless, the variations in chemical shifts between different species remain relatively small, and the values agree with experiments due to the cancellation of SIE. A notable observation is that the chemical shifts of the 2s and 2p electrons are similar, indicating a perturbation caused by the valence electrons. The error in the absolute binding energy of KS ΔSCF against the experiment is nearly constant for the same element in different molecules, and it depends largely on the functional owing to SIE. A shifting scheme previously developed can be employed to reproduce the experimental 2s and 2p binding energies, with dependence on the functional and atom but not on the molecule even for 2s KS ΔSCF binding energies. Upon obtaining the corrected binding energies, we find that the gap between 2s and 2p binding energy is nearly independent of chemical environment for a given element: 57.5, 63.9, and 70.9 eV for the elements P, S, and Cl, respectively.

Douglas-Kroll and infinite order two-component transformations of Dirac-Fock operator.

We extended the conventional Douglas-Kroll (DK) and infinite order two-component (IOTC) methods to a technique applicable to Fock matrices, called extended DK (EDK) and extended IOTC (EIOTC), respectively. First, we defined a strategy to divide the Dirac-Fock operator into zero- and first-order terms. We then demonstrated that the first-order extended DK transformation, which is the Foldy-Wouthuysen transformation for the zero-order term, as well as the second- and third-order EDK and EIOTC, could be well defined. The EDK- and EIOTC-transformed Fock matrix, kinetic energy operator, nuclear attraction operator, and density matrix were derived. These equations were numerically evaluated, and it was found that these methods were accurate. In particular, EIOTC was consistent with the four-component approach. Four-component and extended two-component calculations are more expensive than non-relativistic calculations due to small-component-type two-electron integrals. We developed a new approximation formula, RIS-V, for small-component-type two-electron integrals, including the spin-orbit interaction between electrons. These results suggest that the RIS-V formula effectively accelerates the four-component and extended two-component methods.

REAlgo: Rapid and efficient algorithm for estimating MP2/CCSD energy gradients for large molecular clusters.

This work reports the development of an algorithm for rapid and efficient evaluation of energy gradients for large molecular clusters employing correlated methods viz. second-order Møller-Plesset perturbation theory (MP2) theory and couple cluster singles and doubles (CCSD). The procedure segregates the estimation of Hartree-Fock (HF) and correlation components. The HF energy and gradients are obtained by performing a full calculation. The correlation energy is approximated as the corresponding two-body interaction energy. Correlation gradients for each monomer are approximated from the respective monomer-centric fragments comprising its immediate neighbours. The programmed algorithm is explored for the geometry optimization of large molecular clusters using the BERNY optimizer as implemented in the Gaussian suite of software. The accuracy and efficacy of the method are critically probed for a variety of large molecular clusters containing up to 3000 basis functions, in particular large water clusters. The CCSD level geometry optimization of molecular clusters containing ∼800 basis functions employing a modest hardware is also reported.

Special Topic on High Performance Computing in Chemical Physics.

Computational modeling and simulation have become indispensable scientific tools in virtually all areas of chemical, biomolecular, and materials systems research. Computation can provide unique and detailed atomic level information that is difficult or impossible to obtain through analytical theories and experimental investigations. In addition, recent advances in micro-electronics have resulted in computer architectures with unprecedented computational capabilities, from the largest supercomputers to common desktop computers. Combined with the development of new computational domain science methodologies and novel programming models and techniques, this has resulted in modeling and simulation resources capable of providing results at or better than experimental chemical accuracy and for systems in increasingly realistic chemical environments.

The core ionization energies calculated by delta SCF and Slater's transition state theory.

The core ionization energies of the second-period and third-period elements are studied by ΔSCF and Slater's transition state (STS) theory by using Hartree-Fock (HF) and Kohn-Sham (KS) approximations. Electron correlation increases the estimated core ionization energies, while the self-interaction error (SIE) decreases them, especially for the third-period elements and is a more significant factor. As a result, while HF lacks electron correlation, it is free of SIE and reasonably predicts the core ionization energies. The core ionization energies calculated by HF STS are very close to those calculated by HF ΔSCF, showing that STS reasonably describes the relaxation of the core hole. The core ionization energies calculated by KS are particularly sensitive to the SIE of the functional used, with functionals having less SIE yielding more accurate ΔSCF core ionization energies. Consequently, BH&HLYP gives better results than B3LYP and LC-BOP since BH&HLYP is the hybrid functional with high proportion of the exact HF exchange. Although the core ionization energies are underestimated by ΔSCF due to SIE, STS gives larger core ionization energies than ΔSCF due to a concave behavior of the error curves of STS, which is also related to SIE. The mean absolute deviations of STS relative to ΔSCF, and relative to the experiment, are almost constant regardless of the nuclei among the element in the second period, and likewise among those in the third period. The systematic nature suggests that shifting the STS core ionization energies may be useful. We propose the shifted STS (1) for reproducing ΔSCF values, and the shifted STS (2) to reproduce the observed ones for KS calculations. Both schemes work quite well. The calculated results of KS ΔSCF and STS vary depending on the functional. However, the variation of each species' shifted STS (2) is very small, and all shifted STS (2) values are close to the observed ones. As the shifted STS require only one SCF calculation, they are simple and practical for predicting the core ionization energies.

Protein-ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors.

We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable molecular modeling, approach to perform molecular dynamics simulations, and on an efficient Density Functional Theory (DFT) linear scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme, in particular, by checking the ability of MM and DFT to reproduce results from high-end ab initio computations regarding such inhibitors. The DFT approach enables an a posteriori fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs. We show the necessity of accounting for a large set of plausible protease/inhibitor conformations to generate reliable interaction data. Finally, we point out ways to further improve α-ketoamide inhibitors to more strongly interact with particular protease domains neighboring the active site.

Complexity reduction in density functional theory: Locality in space and energy.

We present recent developments of the NTChem program for performing large scale hybrid density functional theory calculations on the supercomputer Fugaku. We combine these developments with our recently proposed complexity reduction framework to assess the impact of basis set and functional choice on its measures of fragment quality and interaction. We further exploit the all electron representation to study system fragmentation in various energy envelopes. Building off this analysis, we propose two algorithms for computing the orbital energies of the Kohn-Sham Hamiltonian. We demonstrate that these algorithms can efficiently be applied to systems composed of thousands of atoms and as an analysis tool that reveals the origin of spectral properties.

Single-cell dissection, hdWGCNA and deep learning reveal the role of oxidatively stressed plasma cells in ulcerative colitis.

Ulcerative colitis (UC) develops as a result of complex interactions between various cell types in the mucosal microenvironment. In this study, we aim to elucidate the pathogenesis of ulcerative colitis at the single-cell level and unveil its clinical significance. Using single-cell RNA sequencing and high-dimensional weighted gene co-expression network analysis, we identify a subpopulation of plasma cells (PCs) with significantly increased infiltration in UC colonic mucosa, characterized by pronounced oxidative stress. Combining 10 machine learning approaches, we find that the PC oxidative stress genes accurately distinguish diseased mucosa from normal mucosa (independent external testing AUC=0.991, sensitivity=0.986, specificity=0.909). Using MCPcounter and non-negative matrix factorization, we identify the association between PC oxidative stress genes and immune cell infiltration as well as patient heterogeneity. Spatial transcriptome data is used to verify the infiltration of oxidatively stressed PCs in colitis. Finally, we develop a gene-immune convolutional neural network deep learning model to diagnose UC mucosa in different cohorts (independent external testing AUC=0.984, sensitivity=95.9%, specificity=100%). Our work sheds light on the key pathogenic cell subpopulations in UC and is essential for the development of future clinical disease diagnostic tools.