Shape resonance induced electron attachment to cytosine: The effect of aqueous media.

We have investigated the impact of microsolvation on shape-type resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOM-CCSD method in conjunction with the resonance via Padé (RVP) method. Our calculations show that the presence of water molecules causes a redshift in the resonance position and an increase in the lifetime for the three lowest-lying resonance states of cytosine. Furthermore, there are some indications that the lowest resonance state in isolated cytosine may get converted to a bound state in the presence of an aqueous environment. The obtained results are extremely sensitive to the basis set used for the calculations.

State-specific frozen natural orbital for reduced-cost algebraic diagrammatic construction calculations: The application to ionization problem.

We have developed a reduced-cost algebraic diagrammatic construction (ADC) method based on state-specific frozen natural orbital and natural auxiliary functions. The newly developed method has been benchmarked on the GW100 test set for the ionization problem. The use of state-specific natural orbitals drastically reduces the size of the virtual space with a systematically controllable accuracy and offers a significant speedup over the standard ionization potential (IP)-ADC(3) method. The accuracy of the method can be controlled by two thresholds and nearly a black box to use. The inclusion of the perturbative correction significantly improves the accuracy of the calculated IP values, and the efficiency of the method has been demonstrated by calculating the IP of a molecule with 60 atoms and more than 2216 basis functions.

Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials.

Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.

Electron Attachment to DNA: The Protective Role of Amino Acids.

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Electron Attachment to Wobble Base Pairs.

We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.

A low-cost four-component relativistic equation of motion coupled cluster method based on frozen natural spinors: Theory, implementation, and benchmark.

We present the theory and the implementation of a low-cost four-component relativistic equation of motion coupled cluster method for ionized states based on frozen natural spinors. A single threshold (natural spinor occupancy) can control the accuracy of the calculated ionization potential values. Frozen natural spinors can significantly reduce the computational cost for valence and core-ionization energies with systematically controllable accuracy. The convergence of the ionization potential values with respect to the natural spinor occupancy threshold becomes slower with the increase in basis set dimension. However, the use of a natural spinor threshold of 10-5 and 10-6 gives excellent agreement with experimental results for valence and core ionization energies, respectively.

Pair Natural Orbital Equation-of-Motion Coupled-Cluster Method for Core Binding Energies: Theory, Implementation, and Benchmark.

We present the theory and implementation of a lower scaling core-valence separated equation-of-motion coupled-cluster approach based on domain-based local pair natural orbitals for core binding energies. The accuracy of the new method has been compared with that of the standard equation-of-motion coupled-cluster method and experimentally measured results. The use of pair natural orbitals significantly reduces the computation cost and can be applied to large molecules.

A reduced cost four-component relativistic coupled cluster method based on natural spinors.

We present the theory, implementation, and benchmark results for a frozen natural spinors based reduced cost four-component relativistic coupled cluster method. The natural spinors are obtained by diagonalizing the one-body reduced density matrix from a relativistic second-order Møller-Plesset calculation based on a four-component Dirac-Coulomb Hamiltonian. The correlation energy in the coupled cluster method converges more rapidly with respect to the size of the virtual space in the frozen natural spinor basis than that observed in the standard canonical spinors obtained from the Dirac-Hartree-Fock calculation. The convergence of properties is not smooth in the frozen natural spinor basis. However, the inclusion of the perturbative correction smoothens the convergence of the properties with respect to the size of the virtual space in the frozen natural spinor basis and greatly reduces the truncation errors in both energy and property calculations. The accuracy of the frozen natural spinor based coupled cluster methods can be controlled by a single threshold and is a black box to use.

A similarity transformed second-order approximate coupled cluster method for the excited states: Theory, implementation, and benchmark.

We present a novel and cost-effective approach of using a second similarity transformation of the Hamiltonian to include the missing higher-order terms in the second-order approximate coupled cluster singles and doubles (CC2) model. The performance of the newly developed ST-EOM-CC2 model has been investigated for the calculation of excitation energies of valence, Rydberg, and charge-transfer excited states. The method shows significant improvement in the excitation energies of Rydberg and charge-transfer excited states as compared to the conventional CC2 method while retaining the good performance of the latter for the valence excited state. This method retains the charge-transfer separability of the charge-transfer excited states, which is a significant advantage over the traditional CC2 method. A second order many-body perturbation theory variant of the new method is also proposed.

A Core-Valence Separated Similarity Transformed EOM-CCSD Method for Core-Excitation Spectra.

We present the theory and implementation of a core-valence separated similarity transformed EOM-CCSD (STEOM-CCSD) method for K-edge core excitation spectra. The method can select an appropriate active space using CIS natural orbitals and near "black box" to use. The second similarity transformed Hamiltonian is diagonalized in the space of single excitation. Therefore, the final diagonalization step is free from the convergence problem arising due to the coupling of the core-excited states with the continuum of doubly excited states. Convergence trouble can appear for the preceding core-ionized state calculation in STEOM-CCSD. A core-valence separation (CVS) scheme compatible with the natural orbital based active space selection (CVS-STEOM-CCSD-NO) is implemented to overcome the problem. The CVS-STEOM-CCSD-NO has a similar accuracy to that of the standard CVS-EOM-CCSD method but comes with a lower computational cost. The modification required in the CVS scheme to make use of the CIS natural orbital is highlighted. The suitability of the CVS-STEOM-CCSD-NO method for chemical application is demonstrated by simulating the K-edge spectra of glycine and thymine.

Doorway Mechanism for Electron Attachment Induced DNA Strand Breaks.

We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ*-type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism can explain the relative rates of electron attachment induced bond cleavages in genetic materials.

An efficient Fock space multi-reference coupled cluster method based on natural orbitals: Theory, implementation, and benchmark.

We present a natural orbital-based implementation of the intermediate Hamiltonian Fock space coupled-cluster method for the (1, 1) sector of Fock space. The use of natural orbitals significantly reduces the computational cost and can automatically choose an appropriate set of active orbitals. The new method retains the charge transfer separability of the original intermediate Hamiltonian Fock space coupled-cluster method and gives excellent performance for valence, Rydberg, and charge-transfer excited states. It offers significant computational advantages over the popular equation of motion coupled cluster method for excited states dominated by single excitations.

Electron Attachment to Cytosine: The Role of Water.

We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.

Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study.

We present an explicit solvation protocol for the calculation of electron affinity values of the solvated nucleobases. The protocol uses a quantum mechanics/molecular mechanics (QM/MM) approach based on the newly implemented domain-based pair natural orbital EOM-CCSD (equation-of-motion coupled-cluster single-double) method. The stability of the solvated nucleobase anion is sensitive to the local distribution of the water molecules around the nucleobase, and the calculated electron affinity values converge slowly with respect to the number of snapshots and the size of the water box. The use of nonpolarizable water molecules leads to an overestimation of the electron affinity and makes the result sensitive to the size of the QM region in the QM/MM calculation. The electron affinity values, although sensitive to the size of the basis set, lead to an almost constant blue shift of the electron affinity upon the increase in the basis set. The present protocol allows for a controllable description of the various parameters affecting the electron affinity value, and the calculated adiabatic electron affinity values are in excellent agreement with experimental results.

Water mediated electron attachment to nucleobases: Surface-bound vs bulk solvated electrons.

We have presented a mechanism for electron attachment to solvated nucleobases using accurate wave-function based hybrid quantum/classical (QM/MM) simulations and uracil as a test case. The initial electron attached state is found to be localized in the bulk water, and this water-bound state acts as a doorway to the formation of the final nucleobase bound state. The electron transfer from water to uracil takes place because of the mixing of electronic and nuclear degrees of freedom. The water molecules around the uracil stabilize the uracil-bound anion by creating an extensive hydrogen-bonding network and accelerate the rate of electron attachment to uracil. The complete transfer of the electron from water to the uracil occurs in a picosecond time scale, which is consistent with the experimentally observed rate of reduction of nucleobases in the presence of water. The degree of solvation of the aqueous electron can lead to a difference in the initial stabilization of the uracil-bound anion. However, the anions formed due to the attachment of both surface-bound and bulk-solvated electrons behave similarly to each other at a longer time scale.

A Multilayer Approach to the Equation of Motion Coupled-Cluster Method for the Electron Affinity.

We have presented a multilayer implementation of the equation of motion coupled-cluster method for the electron affinity, based on local and pair natural orbitals. The method gives consistent accuracy for both localized and delocalized anionic states and results in many-fold speed-up as compared to the canonical and DLPNO-based implementation of the EA-EOM-CCSD method. We have also developed an explicit fragment-based approach which can lead to even higher speed-up with little loss in accuracy. The multilayer method can be used to treat the environmental effect of both bonded and nonbonded nature on the electron attachment process in large molecules.

Interactions of Solvated Electrons with Nucleobases: The Effect of Base Pairing.

We have investigated the effect of base pairing on the electron attachment to nucleobases in bulk water, taking the guanine-cytosine (GC) base pair as a test case. The presence of the complementary base reinforces the stabilization effect provided by water and preferentially stabilizes the anion by hydrogen bonding. The electron attachment in bulk-solvated GC happens through a doorway mechanism, where the initial electron attached state is water bound, and it subsequently gets converted to a GC bound state. The additional electron in the final GC bound state is localized on the cytosine, similar to that in the gas phase. The transfer of the electron from the initial water-bound state to the final GC bound state happens due to the mixing of electronic and nuclear degrees of freedom and takes place at a picosecond time scale.

Electron Attachment to DNA Base Pairs: An Interplay of Dipole- and Valence-Bound States.

We have investigated the electron-attached states in Watson-Crick guanine-cytosine and adenine-thymine base pairs using the highly accurate equation-of-motion coupled-cluster (EOM-CC) method and extended basis sets. Both base pairs have two bound anionic states. The dipole-bound state is stable even at the neutral geometry, but the valence-bound state is only adiabatically bound. The initial electron attachment results in the formation of a dipole-bound state that acts as a doorway to the valence-bound anionic state. The adiabatic potential energy surface of ground and first excited states of an anion shows an avoided crossing, indicating mixing of the electronic and nuclear degrees of freedom. We have calculated the coupling strength between the valence- and dipole-bound states by fitting a simple diabatic model potential to a cut through the two adiabatic surfaces of the anions obtained from the EOM-CC calculations. The transfer of the electron from the initial dipole-bound to the final valence-bound state has been found to happen at an ultrafast time scale.

Ruthenium-Chelated Non-Innocent Bis(heterocyclo)methanides: A Mimicked ß-Diketiminate.

The unexplored substrate-based reactivity profile of newly designed bis(heterocyclo)methanide (BHM, L1-L3), a structural mimic of ubiquitous ß-diketiminate, was demonstrated on an electronically rich {Ru(acac)2} platform (acac = σ-donating acetylacetonate). In this regard, this work deals with structurally characterized [Ru(L)(acac)2] complexes 1A-3A incorporating electronically varying heterocycles {1A, L1 = bis(imidazo[1,5-a]pyridin-3-yl)methanide; 2A, L2 = (Z)-4-[(6,7-dihydrothieno[3,2-c]pyridin-4-yl)methylene]-6,7-dihydro-4H-thieno[3,2-c]pyridin-5-ide; 3A, L3 = (Z)-6-chloro-1-[(6-chloro-3,4-dihydroisoquinolin-1-yl)methylene]-3,4-dihydro-1H-isoquinolin-2-ide}. The significant impact of electronic modification at the BHM backbone (L1-L3) on its redox tunability at the metal-ligand interface in 1A-3A and its subsequent oxygenation profile to yield bis(heterocyclo)methanone (BMO, analogue of α-ketodiimine) in the corresponding [Ru(BMO)(acac)2] (1B-3B) via a radical pathway were rationalized. In addition, oxidative dehydrogenation of metalated BMO in 1B-3B to BAM [bis(heteroaryl)methanone] in [Ru(BAM))(acac)2] (1C-3C) was illustrated in support of the nonspectator behavior of α-ketodiimine. A combined experimental and theoretical investigation extended mechanistic outlines of the aforementioned transformation processes, which in effect provided a new dimension relating to the analogous ß-diketiminate as well as α-ketodiimine chemistry.

A domain-based local pair natural orbital implementation of the equation of motion coupled cluster method for electron attached states.

This work describes a domain-based local pair natural orbital (DLPNO) implementation of the equation of motion coupled cluster method for the computation of electron affinities (EAs) including single and double excitations. Similar to our earlier work on ionization potentials (IPs), the method reported in this study uses the ground state DLPNO framework and extends it to the electron attachment problem. While full linear scaling could not be achieved as in the IP case, leaving the Fock/Koopmans' contributions in the canonical basis and using a tighter threshold for singles PNOs allows us to compute accurate EAs and retain most of the efficiency of the DLPNO technique. Thus as in the IP case, the ground state truncation parameters are sufficient to control the accuracy of the computed EA values, although a new set of integrals for singles PNOs must be generated at the DLPNO integral transformation step. Using standard settings, our method reproduces the canonical results with a maximum absolute deviation of 49 meV for bound states of a test set of 24 molecules. Using the same settings, a calculation involving more than 4500 basis functions, including diffuse functions, takes four days on four cores, with only 48 min spent in the EA module itself.