Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine.

Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.

Beyond Born-Oppenheimer Constructed Diabatic Potential Energy Surfaces for HeH2.

First-principles based beyond Born-Oppenheimer theory has been employed to construct multistate global Potential-Energy Surfaces (PESs) for the HeH2+ system by explicitly incorporating the Nonadiabatic Coupling Terms (NACTs). Adiabatic PESs and NACTs for the lowest four electronic states (12A', 22A', 32A' and 42A') are evaluated as functions of hyperangles for a grid of fixed values of the hyperradius in hyperspherical coordinates. Conical intersection between different states are validated by integrating the NACTs along appropriately chosen contours. Subsequently, adiabatic-to-diabatic (ADT) transformation angles are determined by solving the ADT equations to construct the diabatic potential matrix for the HeH2+ system which are smooth, single-valued, continuous, and symmetric and are suitable for performing accurate scattering calculations for the titled system.

Construction of Beyond Born-Oppenheimer Based Diabatic Surfaces and Generation of Photoabsorption Spectra: The Touchstone Pyrazine (C4 N2 H4 ).

We construct theoretically "exact" and numerically "accurate" Beyond Born-Oppenheimer (BBO) based diabatic potential energy surfaces (PESs) of pyrazine (C4 N2 H4 ) molecule involving lowest four excited adiabatic PESs (S1 to S4 ) and nonadiabatic coupling terms (NACTs) among those surfaces as functions of nonadiabatically active normal modes (Q1 , Q6a , Q9a and Q10a ) to compute its photoabsorption (PA) spectra. Those adiabatic PESs are calculated using CASSCF as well as MRCI based methodologies, where NACTs are obtained from CP-MCSCF approach. Employing ab initio quantities (adiabatic PESs and NACTs), it is possible to depict the conical intersections (CIs) and develop matrices of diabatic PESs over six normal mode planes. Once single-valued, smooth, symmetric and continuous 2×2 and 4×4 diabatic surface matrices are in hand for the first time, such matrices are used to perform multi-state multi-mode nuclear dynamics with the aid of Time-Dependent Discrete Variable Representation (TDDVR) methodology initializing the product type wavefunction on 1 1 B 1 u ${{1}^{1}{B}_{1u}}$ (S1 ) and 1 1 B 2 u ${{1}^{1}{B}_{2u}}$ (S2 ) states to obtain the corresponding PA spectra. TDDVR calculated spectra for those states (S1 and S2 ) obtained from BBO based 2×2 and 4×4 diabatic surface matrices show good and better agreement with the experimental results, respectively. Both of these calculated results depict better peak progression over the existing profiles of Multi-Configuration Time-Dependent Hartree (MCTDH) dynamics over 2×2 Vibronic Coupling Model (VCM) Hamiltonian.

Photochemistry of 3,6-Didehydropyridazine Biradical─An Untraceable Para Benzyne Analogue.

We report matrix isolation infrared spectroscopic studies to characterize 3,6-didehydropyridazine 6, a heterocyclic analogue of para benzyne, combined with computations. In this regard, we have utilized 3,6-diiodopyridazine 11 as a photolytic precursor. The experiments toward the generation of the biradical are carried out in argon and nitrogen matrices at 4 K. Instead of the elusive biradical, we have observed a ring-opening product maleonitrile (Z)-7 upon irradiation at 254 nm. In contrast, prolonged irradiation at 254 nm leads only to Z-E isomerization, forming fumaronitrile (E)-7. The mechanistic aspects of ring-opening, product selectivity, and Z-E photoisomerization steps have been investigated in detail using high-level ab initio computations. These studies have found that 3,6-didehydropyridazine 6 is an untraceable intermediate, and the ring-opening step leading to maleonitrile is barrierless. In addition, we have proposed the involvement of the S1 (π-π*) state via conical intersection in the Z-E photoisomerization of maleonitrile.

Beyond Born-Oppenheimer based diabatic surfaces of 1,3,5-C6H3F3+ to generate the photoelectron spectra using time-dependent discrete variable representation approach.

In this article, Beyond Born-Oppenheimer (BBO) treatment is implemented to construct diabatic potential energy surfaces (PESs) of 1,3,5-C6H3F3+ over a series [eighteen (18)] of two-dimensional (2D) nuclear planes constituted with eleven normal modes (Q2, Q9x, Q9y, Q13x, Q13y, Q18x, Q18y, Q10x, Q10y, Q12x and Q12y) to include all possible nonadiabatic interactions among six coupled electronic states (X̃2E'', , B̃2E' and ). We had formulated explicit expressions of adiabatic to diabatic transformation (ADT) equations [S. Mukherjee, J. Dutta, B. Mukherjee, S. Sardar and S. Adhikari, J. Chem. Phys., 2019, 150, 064308] for the same system forming six state sub-Hilbert space and at present, these ADT equations are solved by incorporating MRCI level ab initio adiabatic PESs and CP-MCSCF calculated nonadiabatic coupling terms (NACTs) to derive diabatic PESs and couplings. Such single-valued, smooth, symmetric and continuous diabatic surface matrices are utilized to carry out multi-state multi-mode nuclear dynamics with the help of time-dependent discrete variable representation (TDDVR) methodology to compute the photoelectron (PE) spectra of 1,3,5-C6H3F3. Our theoretically calculated spectra for X̃2E'', and states using BBO treatment and TDDVR dynamics show peak by peak correspondence with the experimental results as well as better than the findings of the multi-configuration time-dependent Hartree (MCTDH) method.

Jahn-Teller Effect in Orthorhombic Manganites: Ab Initio Hamiltonian and Roto-vibrational Spectrum.

For the first time, using three different electronic structure methodologies, namely, CASSCF, RS2c, and MRCI(SD), we construct ab initio adiabatic potential energy surfaces (APESs) and nonadiabatic coupling term (NACT) of two electronic states (5Eg) of MnO69- unit, where eight such units share one La atom in LaMnO3 crystal. While fitting those APESs with analytic functions of normal modes (Qx, Qy), an empirical scaling factor is introduced considering the mass ratio of eight MnO69- units with and without one La atom to explore the environmental (mass) effect on MnO69- unit. When the roto-vibrational levels of MnO69- Hamiltonian are calculated, peak positions computed from ab initio constructed excited APESs are found to be enough close with the experimental satellite transitions [ J. Exp. Theor. Phys. 2016, 122, 890-901] endorsing our earlier model results [ J. Chem. Phys. 2019, 150, 064703]. In order to explore the electron-nuclear coupling in an alternate way, theoretically "exact" and numerically "accurate" beyond Born-Oppenheimer (BBO) theory based diabatic potential energy surfaces (PESs) of MnO69- are constructed to generate the photoelectron (PE) spectra. The PE spectral band also exhibits good peak by peak correspondence with the higher satellite transitions in the dielectric function spectra of the LaMnO3 complex.

A beyond Born-Oppenheimer treatment of C6H6 + radical cation for diabatic surfaces: Photoelectron spectra of its neutral analog using time-dependent discrete variable representation.

We employ theoretically "exact" and numerically "accurate" Beyond Born-Oppenheimer (BBO) treatment to construct diabatic potential energy surfaces (PESs) of the benzene radical cation (C6H6 +) for the first time and explore the workability of the time-dependent discrete variable representation (TDDVR) method for carrying out dynamical calculations to evaluate the photoelectron (PE) spectra of its neutral analog. Ab initio adiabatic PESs and nonadiabatic coupling terms are computed over a series of pairwise normal modes, which exhibit rich nonadiabatic interactions starting from Jahn-Teller interactions and accidental conical intersections/seams to pseudo Jahn-Teller couplings. Once the electronic structure calculation is completed on the low-lying five doublet electronic states (X̃2E1g, B̃2E2g, and C̃2A2u) of the cationic species, diabatization is carried out employing the adiabatic-to-diabatic transformation (ADT) equations for the five-state sub-Hilbert space to compute highly accurate ADT angles, and thereby, single-valued, smooth, symmetric, and continuous diabatic PESs and couplings are constructed. Subsequently, such surface matrices are used to perform multi-state multi-mode nuclear dynamics for simulating PE spectra of benzene. Our theoretical findings clearly depict that the spectra for X̃2E1g and B̃2E2g-C̃2A2u states obtained from BBO treatment and TDDVR dynamics exhibit reasonably good agreement with the experimental results as well as with the findings of other theoretical approaches.

The role of electron-nuclear coupling on multi-state photoelectron spectra, scattering processes and phase transitions.

We present first principle based beyond Born-Oppenheimer (BBO) theory and its applications on various models as well as realistic spectroscopic and scattering processes, where the Jahn-Teller (JT) theory is brought in conjunction with the BBO approach on the phase transition of lanthanide complexes. Over one and half decades, our development of BBO theory is demonstrated with ab initio calculations on representative molecules of spectroscopic interest (NO2 radical, Na3 and K3 clusters, NO3 radical, C6H6+ and 1,3,5-C6H3F3+ radical cations) as well as triatomic reactive scattering processes (H+ + H2 and F + H2). Such an approach exhibits the effect of JT, Renner-Teller (RT) and pseudo Jahn-Teller (PJT) type of interactions. While implementing the BBO theory, we generate highly accurate diabatic potential energy surfaces (PESs) to carry out quantum dynamics calculation and find excellent agreement with experimental photoelectron spectra of spectroscopic systems and cross-sections/rate constants of scattering processes. On the other hand, such electron-nuclear couplings incorporated through JT theory play a crucial role in dictating higher energy satellite transitions in the dielectric function spectra of the LaMnO3 complex. Overall, this article thoroughly sketches the current perspective of the BBO approach and its connection with JT theory with various applications on physical and chemical processes.

Beyond Born-Oppenheimer constructed diabatic potential energy surfaces for F + H2 reaction.

First principles based beyond Born-Oppenheimer theory has been implemented on the F + H2 system for constructing multistate global diabatic Potential Energy Surfaces (PESs) through the incorporation of Nonadiabatic Coupling Terms (NACTs) explicitly. The spin-orbit (SO) coupling effect on the collision process of the F + H2 reaction has been included as a perturbation to the non-relativistic electronic Hamiltonian. Adiabatic PESs and NACTs for the lowest three electronic states (12A', 22A', and 12A″) are determined in hyperspherical coordinates as functions of hyperangles for a grid of fixed values of the hyperradius. Jahn-Teller (JT) type conical intersections between the two A' states translate along C2v and linear geometries in F + H2. In addition, A' and A″ states undergo Renner-Teller (RT) interaction at collinear configurations of this system. Both JT and RT couplings are validated by integrating NACTs along properly chosen contours. Subsequently, we have solved adiabatic-to-diabatic transformation (ADT) equations to evaluate the ADT angles for constructing the diabatic potential matrix of F + H2, including the SO coupling terms. The newly calculated diabatic PESs are found to be smooth, single-valued, continuous, and symmetric and can be invoked for performing accurate scattering calculations on the F + H2 system.

ADT: A Generalized Algorithm and Program for Beyond Born-Oppenheimer Equations of "N" Dimensional Sub-Hilbert Space.

The major bottleneck of first principle based beyond Born-Oppenheimer (BBO) treatment originates from large number and complicated expressions of adiabatic to diabatic transformation (ADT) equations for higher dimensional sub-Hilbert spaces. In order to overcome such shortcoming, we develop a generalized algorithm, "ADT" to generate the nonadiabatic equations through symbolic manipulation and to construct highly accurate diabatic surfaces for molecular processes involving excited electronic states. It is noteworthy to mention that the nonadiabatic coupling terms (NACTs) often become singular (removable) at degenerate point(s) or along a seam in the nuclear configuration space (CS) and thereby, a unitary transformation is required to convert the kinetically coupled (adiabatic) Hamiltonian to a potentially (diabatic) one to avoid such singularity(ies). The "ADT" program can be efficiently used to (a) formulate analytic functional forms of differential equations for ADT angles and diabatic potential energy matrix and (b) solve the set of coupled differential equations numerically to evaluate ADT angles, residue due to singularity(ies), ADT matrices, and finally, diabatic potential energy surfaces (PESs). For the numerical case, user can directly provide ab initio data (adiabatic PESs and NACTs) as input files to this software or can generate those input files through in-built python codes interfacing MOLPRO followed by ADT calculation. In order to establish the workability of our program package, we selectively choose six realistic molecular species, namely, NO2 radical, H3+, F + H2, NO3 radical, C6H6+ radical cation, and 1,3,5-C6H3F3+ radical cation, where two, three, five and six electronic states exhibit profound nonadiabatic interactions and are employed to compute diabatic PESs by using ab initio calculated adiabatic PESs and NACTs. The "ADT" package released under the GNU General Public License v3.0 (GPLv3) is available at https://github.com/AdhikariLAB/ADT-Program and also as the Supporting Information of this article.

Aluminum containing molecular bowls and pyridinophanes: use of pyridine modules to access different molecular topologies.

Molecular topologies varying from simple complexes to pyridinophanes (neutral and cationic) and to bicyclic pyridinophane containing organoaluminum (Al-Me) species were synthesized by varying the relative stoichiometry of bis(trimethylsilyl)-N,N'-2,6-diaminopyridine (bap) and the reactive partner (AlMe3). The ultimate goal of these reactions was to systematically design cyclic structures containing group 13 elements. To highlight the reaction potential of these shapes, the bowl-shaped pyridinophane was reacted with the Lewis acid, B(C6F5)3, to generate a stable cationic derivative. An unprecedented bicyclic pyridinophane, [2,6-(Me3SiN)2C5H3N]3Al2, was obtained from the reaction of bap with AlH3·NMe2Et. The formation of [2,6-(Me3SiN)2C5H3N]3Al2 is in contrast to the known reaction between BH3·SMe2 and bap that afforded the syn-tetraazadibora[3.3](2,6)pyridinophane. Quantum chemical calculations have been performed to rationalize the preference for the formation of B-pyridinophane and Al-bicyclic pyridinophane and can be attributed to the nature of B-N and Al-N bonds.

Electronically Unsaturated Three-Coordinate Aluminum Hydride and Organoaluminum Cations.

New three-coordinate and electronically unsaturated aluminum hydride [LAlH]+ [HB(C6 F5 )3 ]- (LH=[{(2,6-iPr2 C6 H3 N)P(Ph2 )}2 N]H) and aluminum methyl [LAlMe]+ [MeB(C6 F5 )3 ]- cations have been prepared. The quantitative estimation of Lewis acidity by Gutmann-Beckett method revealed [LAlH]+ [HB(C6 F5 )3 ]- to be better Lewis acid than B(C6 F5 )3 and AlCl3 making these compounds ideal catalysts for Lewis acid-mediated reactions. To highlight that the work is of fundamental importance, catalytic hydroboration of aliphatic and aromatic aldehydes and ketones have been demonstrated. Important steps of the catalytic cycle have been probed by using multinuclear NMR measurements, including successful characterization of the proposed aluminum benzyloxide cationic intermediate, [LAl-O-CH2 Ph]+ [HB(C6 F5 )3 ]- . The proposed catalytic cycle has been found to be consistent with experimental observations and computational studies clearly indicating the migration of hydride from cationic aluminum center to the carbonyl carbon is the rate-limiting step of the catalytic cycle.

Two Different Pathways in the Reduction of [(S=)PCl(µ-NtBu)]2 with Na.

Reduction of the cyclodiphosphazane [(S=)ClP(µ-NtBu)]2 (1) with sodium metal in refluxing toluene proceeds via two different pathways. One is a Wurtz-type pathway involving elimination of NaCl from 1 followed by head-to-tail cyclization to give the hexameric macrocycle [(µ-S)P(µ-NtBu)2 P(=S)]6 (2). The other pathway involves reduction of the P=S bonds of 1 to generate colorless singlet biradicaloid dianion trans-[S-P(Cl)(µ-NtBu)]2 (2-) , which is observed in the polymeric structures of three-dimensional [{(S-)ClP(µ-NtBu)2 PCl(S)}Na(Na⋅THF2 )]n (3) and two dimensional [{(S-)ClP(µ-NtBu)2 PCl(S)} (Na⋅THF)2 ]n (4).

Reactivity of a dihydroboron species: synthesis of a hydroborenium complex and an expedient entry into stable thioxo- and selenoxo-boranes.

The reaction of a recently synthesized dihydroboron species complexed with bis(phosphinimino)amide, LBH2 (), (L = [N(Ph2PN(2,4,6-Me3C6H2))2](-)) with 3 equivalents of BH2Cl·SMe2 or one equivalent of BCl3 affords the first stable monohydridoborenium ion, [LBH](+)[HBCl3](-) () that is stable without a weakly coordinating bulky anion. Compound can also be prepared directly by refluxing LH with 3 equivalents of BH2Cl·SMe2. Interestingly, reaction of LBH2 () with elemental sulfur and selenium involves oxidative addition of S and Se into B-H bonds and subsequent release of H2S (or H2Se) from the intermediate LB(SH)2 (or LB(SeH)2) species forming stable compounds with terminal boron-chalcogen double bonds LB[double bond, length as m-dash]S () and LB[double bond, length as m-dash]Se (). The electronic structures of compounds , and were elucidated by high resolution mass spectrometry, multi-nuclear NMR and single crystal X-ray diffraction studies. Ab initio calculations on are in excellent agreement with its experimental structure and clearly support the existence of the boron-sulfur double bond.