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We present an approximate approach for the calculation of ionization potential (IP) and electron affinity (EA) by exploiting the complementary energy non-linearity errors for a species M and its one-electron-ionized counterpart (M

We performed 10 ns scale molecular dynamics simulations of 6 SARS-CoV-2 main protease/alpha-ketoamide inhibitor complexes in aqueous solution, in the phase before the inhibitor covalently binds to the protease's catalytic cysteine, using a polarizable multi-scale molecular modeling approach. For each simulation, 100 Mpro/inhibitor snapshots(about 4 800 atoms) were extracted along the last 2 ns simulation segments. They were post processed using a fully quantum mechanical O(N) approach to decompose the protease in sets of fragments from which we computed the mean local interaction energies between the inhibitors and the different pockets of the protease catalytic domain. Contrary to earlier results, our analysis shows that the protease pocket S2 to be a key anchoring site able to lock within the catalytic domain an alpha-ketoamide inhibitor even before covalent bonding to the protease catalytic cysteine occurs. To target that pocket our computations suggest to consider hydrophobic groups, like cyclo-propyl or cyclo-hexyl.

The O2 release of the oxygen-evolving complex of the photosystem II (PSII) is one of the essential processes responsible for the highly efficient O2 production. Despite its importance, the detailed molecular mechanism is still unsolved. In the present study, we show that the O2 release is directly coupled with water insertion into the Mn cluster based on the quantum mechanics/molecular mechanics (QM/MM) calculations. In this mechanism, the O2 molecule first dissociates from the Mn sites in order, that is, the O atom coordinating to the Mn3 (O5a) first dissociates, then the other O atom coordinating to the Mn1 (O5d) dissociates in the next step in the late S4 state (1 → 2). Next, the O2 migrates to a space surrounded by the Val185 and His332 side chains as one water molecule coordinating to the Ca2+ ion (W3) comes into the O2 bonded site (2 → 3). Finally, a pre-S0 state (4) is formed after a proton transfer from the inserted water to the other proton acceptor site (W2) (3 → 4). The highest activation barri...

The answer to the question “Can electron-rich oxygen (O2–) withdraw electrons from metal centers?” is seemingly simple, but how the electron population on the M atom behaves when the O–M distance changes is a matter of controversy. A case study has been conducted for Keggin-type polyoxometalate (POM) complexes, and the first-principles electronic structure calculations were carried out not only for real POM species but also for “hypothetical” ones whose heteroatom was replaced with a point charge. From the results of natural population analysis, it was proven that even an electron-rich O2–, owing to its larger electronegativity as a neutral atom, withdraws electrons when electron redistribution occurs by the change of the bond length. In the case where O2– coexists with a cation having a large positive charge (e.g., P5+(O2–)4 = [PO4]3–), the gross electron population (GEP) on the M atom seemingly increases as the O atom comes closer, but this increment in GEP is not due to the role of the O atom but due t...

We theoretically investigated the physical properties, including the frontier orbital and excitation energies, for thiophene-based semiconducting polymers composed of donor and acceptor units. Orbital analysis revealed that remarkably different behaviors of frontier orbital energies with respect to the degree of polymerization stems from the distribution of the frontier orbitals, which is insightful information for controlling the ionization potentials and electron affinities of semiconducting polymers. We also successfully estimated the frontier orbital energies of the polymers through a simple Huckel theory-based analytical model parametrized from calculations of relatively small oligomers. This simple model allows us to predict the highest occupied molecular orbital–lowest unoccupied molecular orbital gaps of a polymer at a low computational cost. The simulated absorption spectra of the thiophene-based semiconducting polymers were compared with the experimental spectra. The theoretically designed polym...

We have carried out large-scale computational quantum chemistry calculations on the K computer to obtain heats of formation for C60 and some higher fullerenes with the DSD-PBE-PBE/cc-pVQZ double-hybrid density functional theory method. Our best estimated values are 2520.0 ± 20.7 (C60), 2683.4 ± 17.7 (C70), 2862.0 ± 18.5 (C76), 2878.8 ± 13.3 (C78), 2946.4 ± 14.5 (C84), 3067.3 ± 15.4 (C90), 3156.6 ± 16.2 (C96), 3967.7 ± 33.4 (C180), 4364 (C240) and 5415 (C320) kJ mol(-1). In our assessment, we also find that the B3-PW91-D3BJ and BMK-D3(BJ) functionals perform reasonably well. Using the convergence behavior for the calculated per-atom heats of formation, we obtained the formula ΔfH per carbon = 722n(-0.72) + 5.2 kJ mol(-1) (n = the number of carbon atoms), which enables an estimation of ΔfH for higher fullerenes more generally. A slow convergence to the graphene limit is observed, which we attribute to the relatively small proportion of fullerene carbons that are in "low-strain" regions. We further propose that it would take tens, if not hundreds, of thousands of carbons for a fullerene to roughly approach the limit. Such a distinction may be a contributing factor to the discrete properties between the two types of nanomaterials. During the course of our study, we also observe a fairly reliable means for the theoretical calculation of heats of formation for medium-sized fullerenes. This involves the use of isodesmic-type reactions with fullerenes of similar sizes to provide a good balance of the chemistry and to minimize the use of accompanying species.

The geometries and electronic structures of selenolate-protected Au nanoclusters, Au24(SeR)20 and Au20(SeR)16, and their thiolate analogues are theoretically investigated with DFT and SCS-MP2 methods, to elucidate the electronic structure of their unusual Au8 core and the reason why they have the unusual entangled "staple-like" chain ligands. The Au8 core is understood to be an [Au4](2+) dimer in which the [Au4](2+) species has a tetrahedral geometry with a closed-shell singlet ground state. The SCS-MP2 method successfully reproduced the distance between two [Au4](2+) moieties, but the DFT with various functionals failed it, suggesting that the dispersion interaction is crucial between these two [Au4](2+) moieties. The SCS-MP2-calculated formation energies of these nanocluster compounds indicate that the thiolate staple-like chain ligands are more stable than the selenolate ones, but the Au8 core more strongly coordinates with the selenolate staple-like chain ligands than with the thiolate ones. Though Au20(SeR)16 has not been reported yet, its formation energy is calculated to be large, suggesting that this compound can be synthesized as a stable species if the concentration of Au(SeR) is well adjusted. The aurophilic interactions between the staple-like chain ligands and between the Au8 core and the staple-like chain ligand play an important role for the stability of these compounds. Because of the presence of this autophilic interaction, Au24(SeR)20 is more stable than Au20(SeR)16 and the unusual entangled ligands are involved in these compounds.

Near infrared (NIR) fluorescent probes are ideal for in vivo imaging because they offer deeper tissue penetration and lower background autofluorescence. Although most fluorophores in this range are cyanine-based dyes, several new classes of fluorescent NIR probes have been developed. In this study, we developed organic bacteriochlorin derivatives, NMP4 and NMP5, which are excited with a single green light and emit different narrow, well-resolved bands in the NIR (peak of 739 and 770 nm for NMP4 and NMP5, respectively). When conjugated to galactosyl-human serum albumin (hGSA) or glucosyl-human serum albumin (glu-HSA), both targeting H-type lectins, including the β-d-galactose receptor expressing on ovarian cancer, these agents become targeted, activatable, single excitation, multicolor NIR fluorescence probes. After conjugation to either glu-HSA or hGSA, substantial quenching of fluorescence occurs that is reversed after cell binding and internalization. In vitro studies showed higher cancer cell uptake with NMP4 or NMP5 conjugated to hGSA compared to the same conjugates with glu-HSA. In vivo single excitation two-color imaging was performed after intraperitoneal injection of these agents into mice with disseminated ovarian cancer. Excited with a single green light, distinct NIR emission spectra from each fluorophore were detected and could be distinguished with spectral unmixing. In vivo results using a red fluorescence protein (RFP) labeled tumor model of disseminated ovarian cancer demonstrated high sensitivity and specificity for all probes. The success of single excitation, 2-color NIR fluorescence imaging with a new class of bacteriochlorin-based activatable fluorophores, NMP4 and NMP5, paves the way for further exploration of noncyanine dye-based NIR fluorophores.

A new algorithm for massively parallel calculations of electron correlation energy of large molecules based on the resolution of identity second-order Møller-Plesset perturbation (RI-MP2) technique is developed and implemented into the quantum chemistry software NTChem. In this algorithm, a Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model is applied to attain efficient parallel performance on massively parallel supercomputers. An in-core storage scheme of intermediate data of three-center electron repulsion integrals utilizing the distributed memory is developed to eliminate input/output (I/O) overhead. The parallel performance of the algorithm is tested on massively parallel supercomputers such as the K computer (using up to 45 992 central processing unit (CPU) cores) and a commodity Intel Xeon cluster (using up to 8192 CPU cores). The parallel RI-MP2/cc-pVTZ calculation of two-layer nanographene sheets (C150H30)2 (number of atomic orbitals is 9640) is performed using 8991 node and 71 288 CPU cores of the K computer.

The ability to switch optical imaging probes from the quenched (off) to the active state (on) has greatly improved target to background ratios. The optimal activation efficiency of an optical probe depends on complete quenching before activation and complete de-quenching after activation. For instance, monoclonal antibody-indocyanine green (mAb-ICG) conjugates, which are promising agents for clinical translation, are normally quenched but can be activated, when bound to a cell surface receptor and internalized. However, the small fraction of commonly used ICG derivative (ICG-Sulfo-OSu) can bind noncovalently to its mAb and is thus, gradually released from the mAb leading to relatively high background signal especially in the liver and the abdomen. In this study, we re-engineered a mAb-ICG conjugate, (Panitumumab-ICG) using bifunctional ICG derivatives (ICG-PEG4-Sulfo-OSu and ICG-PEG8-Sulfo-OSu) with short polyethylene glycol (PEG) linkers. Higher covalent binding (70–86%) was observed using the bifunctional ICG with short PEG linkers resulting in less in vivo non-covalent dissociation. Panitumumab-ICG conjugates with short PEG linkers were able to detect human epidermal growth factor receptor 1 (EGFR)-positive tumors with high tumor-to-background ratios (15.8 and 6.9 for EGFR positive tumor-to-negative tumor and tumor-to-liver ratios, respectively, at 3 d postinjection).

Four gadolinium (Gd)-based macromolecular contrast agents, G3-(Gd-DOTA)24, G5-(Gd-DOTA)96, G3-(Gd-DTPA)24, and G5-(Gd-DTPA)96, were prepared that varied in the size of dendrimer (generation three and five), the type of chelate group (DTPA or DOTA), and the theoretical number of metallated chelates (24 and 96). Synthesis relied on a dichlorotriazine derivatized with a DOTA or DTPA ligand that was incorporated into the dendrimer and ultimately metallated with Gd ions. Paramagnetic characteristics and in vivo pharmacokinetics of all four contrast agents were investigated. The DOTA-containing agents, G3-(Gd-DOTA)24 and G5-(Gd-DOTA)96, demonstrated exceptionally high r1 relaxivity values at off peak magnetic fields. Additionally, G5-(Gd-DOTA)96 showed increased r1 relaxivity in serum compared to that in PBS, which was consistent with in vivo images. While G3-(Gd-DOTA)24 and G3-(Gd-DTPA)24 were rapidly excreted into the urine, G5-(Gd-DOTA)96 and G5-(Gd-DTPA)96 did not clear as quickly through the kidneys. Molecular simulation of the DOTA-containing dendrimers provides a single-molecular level characterization of the structures and suggests that a majority of the metallated ligands are accessible to water. These triazine dendrimer-based MRI contrast agents exhibit several promising features such as high in vivo r1 relaxivity, desirable pharmacokinetics, and well-defined structure.

Armed antibody-based targeted molecular therapies offer the possibility of effective tumor control with a minimum of side effects. Photoimmunotherapy (PIT) employs a monoclonal antibody-phototoxic phthalocyanine dye, IR700 conjugate that is activated by focal near infrared (NIR) light irradiation after antibody binding to the targeted tumor cell surface leading to rapid necrotic cell death. Therapy by single NIR light irradiation was effective without significant side-effects, however, recurrences were seen in most of treated mice probably because of inhomogeneous distribution of panitumumab-IR700 immuno-conjugate in the tumor, leading to ineffective PIT. We describe here an optimized regimen of effective PIT method for the same HER1-overexpressing tumor model (A431) with fractionated administration of panitumumab-IR700 conjugate followed by systematic repeated NIR light irradiation to the tumor based on timing of antibody redistribution into the remnant tumor under the guidance of IR700 fluorescence signal. Eighty percents of the A431 tumors were eradicated with repeated PIT without apparent side effects and survived with tumor free more than 120 days even after stoping therapy at the day 30. Therapeutic effects were monitored using IR700 fluorescent signal. PIT is a promising highly selective and clinically feasible theranostics for the treatment of MAb-binding tumors with minimal off target effects.

In patients with prostate cancer, a positive surgical margin is associated with an increased risk of cancer recurrence and poorer outcome, yet margin status cannot be determined during the surgery. An in vivo optical imaging probe that could identify the tumor margins during surgery could result in improved outcomes. The design of such a probe focuses on a highly specific targeting moiety and a near-infrared (NIR) fluorophore that is activated only when bound to the tumor. In this study, we successfully synthesized an activatable monoclonal antibody-fluorophore conjugate consisting of a humanized anti-Prostate-Specific Membrane Antigen (PSMA) antibody (J591) linked to an indocyanine green (ICG) derivative. Prior to binding to PSMA and cellular internalization, the conjugate yielded little light; however, after binding an 18-fold activation was observed permitting the specific detection of PSMA+ tumors up to 10 days after injection of a low dose (0.25 mg/kg) of the reagent. This agent demonstrates promise as a method to image the extent of prostate cancer in vivo and could assist with real-time resection of extracapsular extension of tumor and positive lymph nodes.

Anomalous enhancement of stimulated Raman scattering (SRS) of the aromatic CH stretching band was observed when the laser-induced plasma was generated in benzene−toluene mixed solvents. Time-resolv...