Prebiotic chemical origin of biomolecular complementarity.

The early Earth, devoid of the protective stratospheric ozone layer, must have sustained an ambient prebiotic physicochemical medium intensified by the co-existence of shortwave UV photons and very low energy electrons (vLEEs). Consequently, only intrinsically stable molecules against these two co-existing molecular destructors must have proliferated and thereby chemically evolved into the advanced molecules of life. Based on this view, we examined the stability inherent in nucleobases and their complementary pairs as resistance to the molecular damaging effects of shortwave UV photons and vLEEs. This leads to the conclusion that nucleobases could only proliferated as their complementary pairs under the unfavorable prebiotic conditions on early Earth. The complementary base pairing not only enhances but consolidates the intrinsic stability of nucleobases against short-range UV photons, vLEEs, and possibly many as-yet-unknown deleterious agents co-existed in the prebiotic conditions of the early Earth. In short, complementary base pairing is a manifestation of chemical evolution in the unfavorable prebiotic medium created by the absence of the stratospheric ozone layer.

Molecular growth of PANH via intermolecular Coulombic decay.

Nitrogen-bearing polycyclic aromatic hydrocarbons (PANHs) are ubiquitous in space. They are considered precursors to advanced biomolecules identified in meteorites. However, their chemical evolution into biomolecules in photodestructive astrophysical mediums remains a paradox. Here, we show that light can efficiently initiate the molecular mass growth of PANHs. Ultraviolet-photoexcited quinoline monomers, the smallest PANH, were observed to associate and intermolecular Coulombic decay between the associating monomers formed the cations of quinoline-dimer. Molecular rearrangements in the dimer cation lead to a dominant formation of cations heavier than quinoline. The enrichment of these heavier cations over all the other cations reveals the efficiency of this route for the mass growth of PANHs in space. This mechanism also leads to a highly reactive unsaturated PANH-ring via CH loss, a hitherto unknown channel in any photon-driven process. The occurrence of this efficient pathway toward complex molecules points to a rich chemistry in dense interstellar clouds.

Ambient-light-induced intermolecular Coulombic decay in unbound pyridine monomers.

Intermolecular Coulombic decay (ICD) is a process whereby photoexcited molecules relax by ionizing their neighbouring molecules. ICD is efficient when intermolecular interactions are active and consequently it is observed only in weakly bound systems, such as clusters and hydrogen-bonded systems. Here we report an efficient ICD between unbound molecules excited at ambient-light intensities. On the photoexcitation of gas-phase pyridine monomers, well below the ionization threshold and at low laser intensities, we detected the parent and heavier-than-parent cations. The isotropic emission of slow electrons revealed ICD as the underlying process. π-π* excitation in unbounded pyridine monomers triggered an associative interaction between them, which leads to an efficient three-centre ICD. The cation resulting from the molecular association of the three pyridine centres relaxed through fragmentation. This below-threshold ionization under ambient light has implications for the understanding of radiation damage and astrochemistry.

Origin of Resonant Character in the Electron Impact Two-Body Neutral-Fragmentation of Methane.

The observation of peaks in the threshold region of two-body neutral fragmentation of methane molecule, i. e., CH4 →CH3 +H, by low energy electron (LEE) impact has been an enigma. The prevailing explanation that this resonant behavior is due to excitation energy transfer is unsatisfactory since this process is not expected to show peaks in the cross-sections unless there is the involvement of electron-molecule resonances. Our first-principles calculations now reveal that the observed peaks could be explained as due to the formation of negative ion resonances, which dominantly dissociate into two neutral fragments and a free-electron. This case of methane is a pointer to the possibility that such reactions contribute significantly to neutral radical production from molecules by LEE impact in comparison to dissociative electron attachment, and in general could play a significant role in electron-based chemical control.

A Unique QP Partitioning and Siegert Width Using Real-Valued Continuum-Remover Potential.

A simple, practical quantum chemical procedure is presented for computing the energy position and the decay width of autoionization resonances. It combines the L2-stabilized resonance wave function obtained using the real-valued continuum-remover (CR) potential [Y. Sajeev Chem. Phys. Lett. 2013, 587, 105-112] and the Feshbach projection operator (FPO) partitioning technique. Unlike the conventional FPO partitioning of the total wave function into its resonant Q space and background P space components, an explicit partitioning of the total wave function into its interaction region and noninteraction region components is obtained with the help of real-valued continuum-remover potential. The molecular system is initially confined inside a CR potential which removes the electronic continuum of the molecular system in which its resonance state is embedded and, thus, unravels the Q space component of the resonance wave function as a bound, localized eigenstate of the confined system. The eigenfunctions of the molecular Hamiltonian represented in the {1-Q} space constitute a complementary, orthogonal P space. A unique QP partition is obtained when the level-shift of the Q space function due to its coupling with the P space is zero, and the resonance width is computed using these unique partitioned spaces. This new procedure, which we refer to as CR-FPO formalism, is formally very simple and straightforward to implement, yet its applications to the resonance state of a model Hamiltonian and to the doubly excited resonance states of atomic and molecular systems at the full-CI level are very accurate as compared to the alternative, very precise L2 methods. In addition, the CR-FPO formalism is implemented in the multireference configuration interaction (MRCI) method, and uses it for calculating the energy position and the autionization decay width of 2Πg shape resonance in N2-.

Negative Ion Resonance States: The Fock-Space Coupled-Cluster Way.

The negative ion resonance states, which are electron-molecule metastable compound states, play the most important role in free-electron controlled molecular reactions and low-energy free-electron-induced DNA damage. Their electronic structure is often only poorly described but crucial to an understanding of their reaction dynamics. One of the most important challenges to current electronic structure theory is the computation of negative ion resonance states. As a major step forward, coupled-cluster theories, which are well-known for their ability to produce the best approximate bound state electronic eigen solutions, are upgraded to offer the most accurate and effective approximations for negative ion resonance states. The existing Fock-space coupled-cluster (FSCC) and the equation-of-motion coupled-cluster (EOM-CC) approaches that compute bound states are redesigned for the direct and simultaneous determination of both the kinetic energy of the free electron at which the electron-molecule compound states are resonantly formed and the corresponding autodetachment decay rate of the electron from the metastable compound state. This Feature Article reviews the computation of negative ion resonances using the FSCC approach and, in passing, provides the highlights of the equivalent EOM-CC approach.

A hitherto unknown stability of DNA basepairs.

The resonance capture of ubiquitous very low energy electrons (vLEEs) into the π* orbitals of nucleobases is a potential doorway to DNA damage. Our ab initio quantum chemical calculations reveal a possible protection function, which is specific to the complementary basepairing, against such vLEE induced DNA damage.

An Electron Propagator Approach Based on a Multiconfigurational Reference State for the Investigation of Negative-Ion Resonances Using a Complex Absorbing Potential Method.

Negative-ion resonances are important metastable states that result from the collision between an electron and a neutral target. The course of many chemical processes in nature is often dictated by how an intermediate resonance state falls apart. This article reports on the development of an electron propagator (EP) based on a Hamiltonian H perturbed by a complex absorbing potential (CAP) and a multiconfigurational self-consistent field (MCSCF) initial state to study these resonances. Perturbation of H by a CAP makes the resonances amenable to a bound-state method like MCSCF. Resonances stand out among the non-resonant states as persistent complex eigenvalues of the perturbed H when the strength (η) of the CAP is varied. The MCSCF method gives a reliable and accurate description of the target states, especially when the non-dynamical correlations are dominant. The resonance energies are obtained from the poles of the EP. We propose three variants of our EP depending on how the effect of the CAP is introduced. We find that the computationally most efficient variant is the one in which the reference state of the EP is an unperturbed MCSCF wavefunction and a non-zero CAP is defined only on the virtual orbital subspace of the reference state. The onset of the CAP is carefully optimized in order to minimize the artifacts due to reflections from the CAP. An extrapolation method (based on a Padé approximant) and a de-perturbation method are adopted in order to account for the limitations of finite basis sets used and determine the resonance energy in the limit of η → 0. 2P Be-, 2Πg N2-, and 2Π CO- shape resonances are investigated. The position and width of these resonances computed in this study agree well with those reported earlier in the literature.

A Concerted Synchronous [2 + 2] Cycloreversion Repair Catalyzed by Two Electrons.

The current understanding of photoenzyme-catalyzed [2 + 2] cycloreversion repair of cyclobutane pyrimidine dimer (CPD) is that a photogenerated electron from the photolyase enzyme catalyzes the repair. This one-electron catalyzed repair is a sequential two-bond breaking cycloreversion of the cyclobutane center and involves a negative ion radical as an intermediate. Here, by resonantly capturing two exogenous low-energy electrons into the molecular field of a CPD, we show that the concerted synchronous two-bond breaking reaction, which is intermediate-free, and hence a safe repair, is feasible through two-electron catalysis.

Formation of CO2 from formic acid through catalytic electron channel.

Low energy electrons can initiate and control chemical reactions through resonant attachment forming an electron-molecule compound state. Recently, it has been theoretically shown that free electrons can also act as catalysts in chemical reactions. We investigate this novel concept for the case of conversion of formic acid into CO2. Resonant production of CO2 from cold formic acid films by low energy electron impact is observed using Fourier transform infrared spectroscopy. The resonant peak observed at 6 eV is identified as the catalytic electron channel. The experimental results are augmented with the ab initio quantum chemical calculations.

Inducing chemical reactivity on specific sites of a molecule using the Coulomb interaction exerted by a low energy electron.

Remarkable site-specificity in the resonant attachment of low energy electrons (LEEs) to molecular targets is proposed as an efficient method for inducing chemical reactivity on specific sites of molecules. The Coulomb interaction between the attached electron and the most polarizable molecular electrons localized on the attached site is the reason for site-specific chemical reactivity. The Coulombically induced site-specific chemical reactivity is best illustrated by the LEE induced chemical transformation of a weakly bound molecular complex into a strong covalent adduct. The chemical transformation occurs due to the Coulombically induced nucleophilicity on a specific molecular moiety in the complex. A simple strategy for inducing site-specific chemical reactivity using a LEE may find new avenues in chemical synthesis.

Communication: Low-energy free-electron driven molecular engineering: In situ preparation of intrinsically short-lived carbon-carbon covalent dimer of CO.

Molecular modification induced through the resonant attachment of a low energy electron (LEE) is a novel approach for molecular engineering. In this communication, we explore the possibility to use the LEE as a quantum tool for the in situ preparation of short lived molecules. Using ab initio quantum chemical methods, this possibility is best illustrated for the in situ preparation of the intrinsically short-lived carbon-carbon covalent dimer of CO from a glyoxal molecule. The chemical conversion of glyoxal to the covalent dimer of CO is initiated and driven by the resonant capture of a near 11 eV electron by the glyoxal molecule. The resulting two-particle one-hole (2p-1h) negative ion resonant state (NIRS) of the glyoxal molecule undergoes a barrierless radical dehydrogenation reaction and produces the covalent dimer of CO. The autoionization electron spectra from the 2p-1h NIRS at the dissociation limit of the dehydrogenation reaction provides access to the electronic states of the CO dimer. The overall process is an example of a catalytic electron reaction channel.

Low energy electron catalyst: the electronic origin of catalytic strategies.

Using a low energy electron (LEE) as a catalyst, the electronic origin of the catalytic strategies corresponding to substrate selectivity, reaction specificity and reaction rate enhancement is investigated for a reversible unimolecular elementary reaction. An electronic energy complementarity between the catalyst and the substrate molecule is the origin of substrate selectivity and reaction specificity. The electronic energy complementarity is induced by tuning the electronic energy of the catalyst. The energy complementarity maximizes the binding forces between the catalyst and the molecule. Consequently, a new electronically metastable high-energy reactant state and a corresponding new low barrier reaction path are resonantly created for a specific reaction of the substrate through the formation of a catalyst-substrate transient adduct. The LEE catalysis also reveals a fundamental structure-energy correspondence in the formation of the catalyst-substrate transient adduct. Since the energy complementarities corresponding to the substrate molecules of the forward and the backward steps of the reversible reactions are not the same due to their structural differences, the LEE catalyst exhibits a unique one-way catalytic strategy, i.e., the LEE catalyst favors the reversible reaction more effectively in one direction. A characteristic stronger binding of the catalyst to the transition state of the reaction than in the initial reactant state and the final product state is the molecular origin of barrier lowering.

Low-energy-electron induced permanently reactive CO2 molecules.

Ab initio quantum chemical studies show that a very weak molecular complexation of CO2 with a dipolar molecule is able to suppress the autoionization of the electron from its transient negative ion states. Since the autoionization is suppressed, the transient negative ion can efficiently relax its geometry to form the reductively activated CO2 moiety. Unlike the reductively activated isolated CO2 molecules, which are deactivated immediately due to their thermodynamic metastability, the reductively activated CO2 moieties of the weak molecular complexes are infinitely long-lived and, hence, permanently reactive.

Continuum remover-complex absorbing potential: Efficient removal of the nonphysical stabilization points.

By adding a negative imaginary potential of variable strength eta to the Hamiltonian, the resonance state of a system can be found as complex energy stabilized points in the eta-trajectories of the eigenvalues. One problem that arises in practical calculations is the appearance of nonphysical complex energy stabilized points. A new method for separating the physical from the nonphysical complex energy stabilized points is proposed. The method is best illustrated with strongly correlated two-electron systems.

Hund's multiplicity rule: from atoms to quantum dots.

In 1965, Davidson has shown that the textbook explanation for the Hund's multiplicity rule in atoms, based on the Pauli principle, is wrong. The reason for the failure of the textbook proof, as has been given later by others and as appears today in modern textbooks, it is based on the need to introduce angular electronic correlation into the calculations. Here, we investigate an applicability of this argumentation for helium and for the case of two-electron spherically symmetric rectangular quantum dots (QDs). We show that, for helium and also for the QD, the differences between the singlet and triplet excited states can be explored by calculations within the framework of the mean-field approximation, and, surprisingly, without the need of introducing the angular electronic correlation. Moreover, our calculations have shown that the triplet state of the QD is lower in energy than the corresponding singlet state due to lower electronic repulsion contribution, exactly as being assumed in the oldest explanation of the Hund's rule based on the Pauli principle.

Reflection-free complex absorbing potential for electronic structure calculations: Feshbach-type autoionization resonances of molecules.

The reflection-free complex absorbing potential (RF-CAP) method has been already applied to the study of the autoionization resonance of helium [Sajeev et al., Chem. Phys. 329, 307 (2006)]. The present work introduces a systematic way for implementing RF-CAP for the electronic structure calculations using Gaussian basis sets for molecules. As a test case study we applied the RF-CAP method to the lowest (1)Sigma(g) (+) and (1)Sigma(u) (+) Feshbach-type autoionization resonances of hydrogen molecule. Since thin RF-CAP absorbs fast electrons much better than the slow ones, a weak dc field has been added to the RF-CAP in the peripheral region of the molecule.

Correlated complex independent particle potential for calculating electronic resonances.

We have formulated and applied an analytic continuation method for the recently formulated correlated independent particle potential [A. Beste and R. J. Bartlett J. Chem. Phys. 120, 8395 (2004)] derived from Fock space multireference coupled cluster theory. The technique developed is an advanced ab initio tool for calculating the properties of resonances in the low-energy electron-molecule collision problem. The proposed method quantitatively describes elastic electron-molecule scattering below the first electronically inelastic threshold. A complex absorbing potential is utilized to define the analytic continuation for the potential. A separate treatment of electron correlation and relaxation effects for the projectile-target system and the analytic continuation using the complex absorbing potential is possible, when an approximated form of the correlated complex independent particle potential is used. The method, which is referred to as complex absorbing potential-based correlated independent particle (CAP-CIP), is tested by application to the well-known (2)Pi(g) shape resonance of e-N(2) and the (2)B(2g) shape resonance of e-C(2)H(4) (ethylene) with highly satisfactory results.