Relaxed Potential Energy Surface Research Articles

On the Diffusion of Ionic Liquids in ILs@ZIF-8 Composite Materials: A Density Functional Theory Study.

Recently, composite materials consisting of ionic liquids (ILs) and metal-organic frameworks (MOFs) have attracted a great deal of attention due to their fantastic properties. Many theoretical studies have been performed on their special structures and gas separation applications. Yet, the mechanism for the diffusion of ILs inside MOF channels still remains unclear. Here, the DFT calculations (e.g., rigid and relaxed potential energy surface, PES, scan) together with frontier orbital analysis, natural charge analysis, and energy decomposition analysis were performed to investigate the diffusion behavior of a typical IL, [C4mim][PF6], into the ZIF-8 SOD cage. The PES profiles indicate that it is quite difficult for the cation [C4min]+ to diffuse into the cage of ZIF-8 through the pristine pores because of the large imidazole steric hindrance, which results in a large energy barrier of ca. 40 kcal·mol-1 at the least. Interestingly, the PES reveals that a successful diffusion could be obtained by thermal contributions, which enlarge the pore size through swing effects at higher temperatures. For example, both [C4mim]+ and [PF6]- could easily diffuse through the channel of the ZIF-8 SOD cage when the pore size was increased to 6.9 Å. Subsequently, electronic structure analyses reveal that the main interactions between [PF6]- or [C4mim]+ and ZIF-8 are the steric repulsion interactions. Finally, the effects of the amounts of [C4mim][PF6] on the ZIF-8 structures were investigated, and the results show that two pairs of [C4mim][PF6] per SOD cage are the most stable in terms of the interaction between energies and structural changes. With these findings, we propose that the high-temperature technique could be employed during the synthesis of IL@MOF membranes, to enrich their family members and their industrial applications.

Time-dependent wave-packet approach to the excited-state intramolecular proton transfer based on relaxed potential energy surfaces of benzimidazole molecule

The wave-packet dynamical approach was used to investigate the excited-state intramolecular proton transfer (PT) of 5′-amino-2-(2′-hydroxyphenyl) benzimidazole (P1) based on the relaxed potential surfaces. For the involved PT process of P1 molecule, the quantum chemical calculation shows that relative to the ground state S0 with a single potential well, the excited state S1 with a double potential well can give much dynamical information. It is also found that because of the existence of a shallow potential barrier on the excited state S1, the PT in it is much easier than that in the ground state S0. When a laser field is used to pump the wave packet and induce the PT process, the external field parameters, such as the frequency and the envelope, also have influences on the PT process because of the impact of both pump time and the energy gap between two states. This kind of external field effect on the PT process gives a specific perspective to examine its dynamical mechanism and provides a reference for exploring the light-induced biophysical processes.

Theoretical Investigations of the Crystal Structures and Molecular Energetics of High Quality Silicon Carbide (β-SiC) Precursor Compound 1,4-bis(trimethylsilyl)benzene

Over the last decades, the rapidly growing theoretical methods have revolutionized whole scientific paradigm, developed state-of-art analyses, and created substantial computational platforms through the huge support of outstanding mathematical algorithms. The self-consistent-charge density-functional based tight-binding (SCC-DFTB) scheme is one of them that offers versatile and efficient quantum mechanical calculations with some unique features compatible especially to the crystalline solid even at low computational resources. Its effective parametrizations and computational implementations under the Gaussian standardized interface as an "External program" via the users' script (Gaussian- External methodology; GEM) has added an additional value because of which various in-built high-level Gaussian computations are directly accessible. Herewith, the Gaussian offered geometry optimization algorithms and convergence criteria plus the ModRedundant type relaxed potential energy surface (PES) scanning techniques are assessed through the GEM, and characterized the crystal structures with concerned molecular energetics and PES of the experimentally synthesized 1,4-bis (trimethylsilyl) benzene (1,4-BTMSB) compound; a potential precursor for the high quality Silicon Carbide (β-SiC) coating particles, and an ideal "Internal Standard" for the quantitative spectroscopic analyses. The general results reveal that the 1,4- BTMSB molecules in its unit-cell and crystal lattice experience significant non-bonding interactions that induces them to attain the definite molecular geometry with recognizable ring, angle, torsional, and steric strains. The quantitative analyses of its PES depict that the phenylene ring has to overcome multiple yet unidentical energy barriers with the tallest Ea1= 5.3 kcal/mol in order to undergo internal 2π angular rotation around the 1,4-(C-Si) axes. And, exhibiting such type internal rotation of its phenylene ring is energetically highly probable as this compound is widely employed in coating high temperature reactors, and in quantizing analyte in high energy run spectroscopic facilities. The same quantification is referred here in order to underscore the significance of adopting perfectly closed topological molecular architectures while designing/synthesizing amphidynamic type crystalline free molecular gyrotops and their prototypes.

The effects of conformation and intermolecular hydrogen bonding on the structure and IR spectra of flutamide; a study based on the matrix isolation technique, ab initio and DFT calculations

In this study, stable conformers of flutamide referred to as an anticancer drug were searched through a relaxed potential energy surface scan carried out at the B3LYP/6-31G(d) level of theory. This was followed by geometry optimization and thermochemistry calculations performed with the HF-SCF, MP2, B3LYP methods and the 6-31G(d), 6–311++G(d,p), aug-cc-pvTZ basis sets for each of the determined minimum energy conformers. The results revealed that flutamide has at least five stable conformers and two of them provide the major contribution to the observed matrix isolation infrared (IR) spectra of the molecule. The effects of conformational variety and intermolecular hydrogen bonding interactions on the observed IR spectra of flutamide were interpreted in the light of the vibrational spectral data obtained for the most stable monomer and dimer forms of the molecule at the same levels of theory. Pulay’s “Scaled Quantum Mechanical-Force Field (SQM-FF)” method was used in the refinement of the calculated harmonic wavenumbers, IR intensities and potential energy distributions. This scaling method which proved its superiority to both anharmonic frequency calculations and other scaling methods helped us to correctly interpret the remarkable differences between the matrix IR spectra of flutamide in argon and the condensed phase IR spectra of the molecule in solvents such as KBr, H2O, D2O, ethanol and methanol.

Rotamers of Methanediol: Composite Ab Initio Predictions of Structures, Frequencies, and Rovibrational Constants

Geminal diols are known to be important intermediates in atmospheric ozonolysis and the aerosol cycle. Recently, the simplest member of this class, methanediol, was interrogated in the gas phase with infrared spectroscopy. To aid in future spectroscopic investigations of methanediol, including in the interstellar medium, we report fundamental frequencies and rovibrational constants for the two rotamers of this molecule using ab initio composite methods along with vibrational perturbation theory. Sensitivity of the predictions to the level of theory and the treatment of anharmonic resonances are carefully assessed. The OH stretching harmonic frequencies of both rotamers are particularly sensitive to the level of theory. The CH stretches of the Cs rotamer are sensitive to the treatment of anharmonic resonances with VPT2-based effective Hamiltonian models. Equilibrium bond distances and harmonic frequencies are converged conservatively to within 0.0005 Å and 3 cm-1, respectively. The effect of tunneling on the rotational constants is investigated with a 2D variational calculation, based on a relaxed hydroxyl torsional potential energy surface. Tunneling is found to be negligible in the lower energy C2 rotamer but should modify the rotational constants of the Cs rotamer on the order of MHz, giving rise to rotational line splittings of the same order. The rovibrational constants of the Cs rotamer are dominated by hydroxyl torsional effects, and here we see evidence for the breakdown of vibrational perturbation theory.

A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part I: Force Field Development.

This work presents a novel parametrization for the ReaxFF formalism as a means to investigate reaction processes of chlorinated organic compounds. Force field parameters cover the chemical elements C, H, O, Cl and were obtained using a novel optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization shows good transferability, as demonstrated on two independent ab initio validation sets. While this first part of our two-paper series focuses on force field parametrization, we apply our parameters to the simulation of chlorinated dibenzofuran formation and decomposition processes in Part II.

Hydrogen-bonding interactions involving the Imidazol-2‑ylidene and its Heavy-atom analogues

The hydrogen-bonded complexes formed between the imidazol-2‑ylidene and its heavier congeners C2H4N2T: (T = C, Si, Ge, Sn, Pb) and the three selected electron acceptors (HF, HCN and C2H2) have been optimized at the aug-cc-pVTZ level, and the nature of these complexes has been investigated by natural bond orbital (NBO), atoms in molecules (AIM) and energy decomposition analyses. The complexes can be classified into type-A structure and type-B structure according to the location of the electron acceptors. The electron acceptors are around T atoms of C2H4N2T: for the type-A complexes, and the electron acceptors are above the five-membered ring (π-system) of C2H4N2T: for the type-B complexes. The electron-donating ability of T atoms becomes weaker, and that of π-systems becomes stronger when T atoms become heavier for C2H4N2T:, which is consistent with the molecular electrostatic potentials (MEP) maps of C2H4N2T:. For a given C2H4N2T:, the Eint values of the type-A complexes go in the order HF > HCN > C2H2, and the Eint values of the type-B complexes go in the order HF ≈ HCN > C2H2. The contribution of electrostatic energy to the interaction energy of complexes becomes smaller for the type-A complexes when the T atoms become heavier. The interaction energies are dominated by the electrostatic energies for all the type-B complexes involving HF, and the interaction energies are dominated by the dispersion energies for most type-B complexes involving HCN and C2H2. The relaxed potential energy surface scans were performed for some selected complexes involving HF and HCN to examine the difference in binding behavior between HF and HCN.

Ab Initio Studies of NMNH(2-) Conformers in Water-Methanol Solutions: Comparative Analysis of the Biexponential Fluorescence Signals for NMNH(2-) and NADH.

Ab initio studies of the structure of reduced β-nicotinamide d-ribonucleotide (NMNH(2-)) conformations in water and methanol solutions have been carried out for clarifying the role of the phosphate groups in fluorescence parameters of the NMNH(2-) molecule and the reduced β-nicotinamide adenine dinucleotide (NADH) molecule. Relaxed potential energy surfaces as a function of the dihedral rotation angle of the amide group in the NMNH(2-) molecule were calculated in the ground electronic state and the first excited electronic state to better understand the effect of phosphate groups on the nonradiative decay rates in the nicotinamide chromophore groups. The differences in the weighting coefficients in the biexponential fluorescence signals for NMNH(2-) and NADH molecules in solution were explained. A strong hydrogen bonding between the amide hydrogen atom and the nearest oxygen O- atom from the phosphate group was detected by ab initio calculations for the folded NMNH(2-) conformations in the ground electronic state at trans configurations of the nicotinamide ring. This hydrogen bonding turned out to be much weaker for the first excited electronic state. These calculated data show that, after optical excitation of the NMNH(2-) molecule, a rapid change in the geometry of the molecule is possible. The strong interaction of the phosphate group with the amide group in NMNH(2-) molecules in aqueous solution leads to the predominance of the folded NMNH(2-) conformations and trans configurations of the nicotinamide ring. This explains the reason for the dominance of one fluorescence decay time of NMNH(2-) in the aqueous solution. Based on these data, an important conclusion can be drawn that the contribution of the exponent with the short decay time τ ≈ 0.28 ns to the fluorescence signal of NMNH(2-), NADH, and NADPH molecules is related to the trans configuration of the nicotinamide ring.

Effects of substituent and excess electron attachment on proton transfer between the radiosensitizer base pairs in aqueous solution

We investigate the proton transfer reaction of radiosensitizing drugs 5-substituted thymine-adenine (5XT-A, X = Br, OCN) in water solutions through the density functional theory (DFT) computations. The relaxed three-dimension potential energy surfaces (PESs) along the two-hydrogen bond of 5XT-A are constructed to reveal the possible proton transfer pathways. The calculations show that the single proton transfer of 5XT-A undergoes a lower energy barrier than that of normal base pair (5OCNT-A < 5BrT-A < T-A). With considering the excess electron attachment, the anion base pair (T-A)- possesses higher energy barrier associated to the proton transfer process. However, the (5XT-A, X = Br, OCN)- anions could dissociate into T•-A radical, which can promote the intermolecular proton transfer reaction between base pairs. It is found that both the neutral and anionic 5-subsituted base pairs can contribute to DNA mutation through the easier proton transfer reaction, which is qualitatively demonstrated by the substituent-induced hydrogen bond enhancement. Our results are helpful to understand the mechanism of enhanced DNA damage in radiotherapy, and are prospective for the design of radiosensitizing drugs without the biotoxicity.

The conformational landscape of myrtenol: The structure of the hydroxymethyl group and its robustness upon hydration.

The conformational landscape of myrtenol (2-pinen-10-ol) and its robustness upon hydration were investigated theoretically and experimentally by employing a synergic combination of quantum chemical calculations and Fourier transform microwave spectroscopy coupled to a supersonic jet expansion. Relaxed potential energy surfaces have been carried out, and the lowest energy conformers of the monomer were found to be associated with different geometries of the hydroxymethyl group from those previously reported [Sedo et al., J. Mol. Spectrosc. 356, 32 (2019)]. Geometry optimizations and harmonic vibrational frequency calculations allowed characterization of the equilibrium structure of the possible conformers of myrtenol. Among the nine predicted structures, four have been observed, analyzed, and identified. The controversy on the geometry was solved with the deuteration of the hydroxyl group, which led to the determination of substitution (rs) geometry, in agreement with the present theoretical results. Interestingly, the four observed conformers exhibit the same orientation of OH as in the allyl alcohol molecule. Furthermore, hydrogen bonding linking myrtenol to water was studied. One monohydrate has been observed and identified. Non-covalent interactions and natural bond orbital analysis were performed to depict the interactions responsible for the stabilization of the observed structure. We conclude that the structure of the hydroxymethyl group is robust and does not change upon hydration.

Thermodynamics and Reaction Mechanisms for Decomposition of a Simple Protonated Tripeptide, H+GGA: From H+GGG to H+GAG to H+GGA.

We present a thorough characterization of fragmentations observed in threshold collision-induced dissociation (TCID) experiments of protonated glycylglycylalanine (H+GGA) with Xe using a guided ion beam tandem mass spectrometer. Kinetic energy dependent cross sections for nine ionic products were obtained and analyzed to provide 0 K barriers for the five primary products, [b2]+, [y1 + 2H]+, [b3]+, [y2 + 2H]+, and [a1]+; and four secondary products, [a2]+, [a3]+, high-energy [y1 + 2H]+, and CH3CHNH2+, after accounting for multiple ion-molecule collisions, the internal energy of reactant ions, unimolecular decay rates, competition between channels, and sequential dissociations. Relaxed potential energy surface scans performed at the B3LYP-GD3BJ/6-311+G(d,p) level of theory are used to identify transition states (TSs) and intermediates of the five primary and three secondary products (with the mechanism of the other secondary product previously established). Geometry optimizations and single point energy calculations of reactants, products, intermediates, and TSs were performed at several levels of theory. These theoretical energies are compared with experimental threshold energies and found to give reasonable agreement, with B3LYP-GD3BJ and M06-2X levels of theory performing slightly better than MP2 and better than B3LYP. The results obtained here are compared with previous results for decomposition of H+GGG and H+GAG to probe the effect of changing the amino acid sequence. Methylation in H+GGA has a significant effect on the competition between the primary sequence products, [b2]+ and [y1 + 2H]+, suppressing the [b2]+ cross section by raising its threshold energy, while enhancing that of [y1 + 2H]+ by lowering its threshold energy.

Higher-Energy Hexafluoroisopropanol···Water Isomer and Its Large Amplitude Motions: Rotational Spectra and DFT Calculations.

Rotational spectra of the 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP)···water complex were measured using a chirped pulse Fourier-transform microwave spectrometer. The spectral analyses, aided by density functional theory calculations, reveal two HFIP···water isomers: one previously reported, trans HFIP (HFIPt)···water (Phys. Chem. Chem. Phys. 2015, 119, 5650-5657), and a new isomer, gauche HFIP (HFIPg)···water. To confirm the identity of the new isomer, rotational spectra of seven of its deuterated species were also measured and analyzed. Both the experimental and theoretical pieces of evidence indicate that the intermolecular interaction with water preferentially stabilizes the HFIPg monomer configuration over the global minimum configuration, HFIPt. The relative energy difference between these monomeric forms is 4.1 kJ mol-1 and decreases to 2.5 kJ mol-1 in the respective monohydrates at the B3LYP-D3(BJ)/def2-QZVP level of theory. Both rigid and relaxed potential energy surface scans were carried out to gain insights into the large-amplitude water motions in HFIPg···water. The nonobservation of a water tunneling splitting in HFIPt···water has been explained to be a result of a barrier-less (after zero-point-energy correction) pathway for the water motion, whereas in HFIPg···water, a relatively large water tunneling barrier was identified as the cause of barely resolved water tunneling splittings. Noncovalent interaction and quantum theory of atoms and molecule analyses were used to evaluate the changes in HFIPg···water when going from the minimum to the transition state in terms of attractive interactions such as the OH···H and OH···F contacts. The effect of fluorination is discussed by comparing the vastly different binding topologies of isopropanol···water and HFIP···water.

Theoretical study on pentiptycene molecular brake: photoinduced isomerization and photoinduced electron transfer.

The isomerization of the double bond plays an important role in the braking and de-braking of the light-controlled molecular brake. Therefore, the pentiptycene-type (Pp-type) light-controlled molecular brake system ((E)- and (Z)-4'-pentiptycyl vinyl-[1,1'-biphenyl]-4-carbonitrile) containing the C = C double bond was theoretically studied. Combining the 6-31G(d) basis set, the ωB97XD functional with dispersion correction was applied to implement the (E)-configuration and (Z)-configuration initial optimization. Next, using the 6-311G(d,p) basis set, the relaxed potential energy surface scans of the rotation angle were operated, and then the optimization calculations of the transition states at the extremum high points. Analyzing the stagnation points and the rotational transition states on the potential energy profiles, the rotation mechanism and basic energy parameters of the molecular brake were obtained. Then, the DFT computations at ground states and the TD-DFT computations of vertical excitation energy were put into practice at the accuracy of the def-TZVP basis set for the two configurations, and using the natural transition orbital (NTO) analyses combining the excitation energies and absorption spectra, the electronic transition characteristics and electron transfer properties of light-controlled molecular brake were studied. Afterwards, in order to investigate the photoinduced isomerization reaction, the C = C double bond was scanned on the relaxed potential energy surface, and the intermediates of the isomerization reaction were searched and analyzed; thus, the braking mechanism of the light-controlled molecular brake was proposed.

Analytical gradients for core-excited states in the algebraic diagrammatic construction (ADC) framework.

Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core-valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn-Teller distorted geometry of the 1s → π* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states.

2‐Hydroxy‐5‐nitropyridine and 5‐nitro‐2‐pyridone: Tautomerism, infrared, Raman, and NMR spectral interpretations, normal coordinate analysis, and DFT calculations

AbstractRaman (3700–50 cm−1) and infrared (IR) (4000–230 cm−1) spectra of 2‐hydroxy‐5‐nitropyridine (HNP; C5H4N2O3) have been recorded in the solid phase in addition to 1H, 13C, and 15N nuclear magnetic resonance (NMR) spectra of the sample in dimethyl sulfoxide‐d6 (DMSO‐d6). Initially, keto and enol tautomeric forms were proposed owing to proton transfer from the hydroxyl group to pyridine nitrogen atom. Quantum mechanical calculations based on density functional theory (DFT; B3LYP, ωB97XD, and mPW1PW91) were carried out using 6‐31G(d) and 6‐311++G(d,p) basis sets favoring keto‐NPO, 5‐nitro‐2‐pyridone, tautomer by ~0.857–1.345 kcal/mol with minor enol‐HNP in the gas phase. Moreover, 1H, 13C, and 15N NMR chemical shifts were predicted using gauge‐invariant atomic orbital‐DFT calculation at 6‐311++G(d,p) basis set using integral equation formalism of the polarization continuum solvation model including solvent effects. The calculated chemical shifts and spin–spin coupling constants (JHH) for keto tautomer better resemble those experimentally observed rather than the enol form. The observed IR/Raman bands were assigned quantitatively to their normal modes based on the calculated vibrational frequencies, force constants in internal coordinates, normal coordinate analysis, and potential energy distributions. Finally, the nitro and hydroxyl barriers to internal rotations were predicted via a relaxed potential energy surface scan using B3LYP/6‐311++G(d,p) calculations. The results are reported herein and compared with similar molecules whenever appropriate.

Network structure and properties of crosslinked bio-based epoxy resin composite: An in-silico multiscale strategy with dynamic curing reaction process

A multiscale simulation strategy was proposed to study the curing reaction on the network formation and corresponding mechanical properties of a bio-based epoxy resin composite. The crosslinking process of the system to form an epoxy network structure was reproduced on the mesoscopic scale by the dissipative particle dynamics simulation coupled with a curing reaction model. The density functional theory (DFT)-based method, IRC and relaxed potential energy surface scanning calculations were combined with the reverse mapping operations in order to improve the overall quality the reverse mapped structures. Finally, molecular dynamics simulations were performed on the atomistic level to analyze the mechanical properties, the volume shrinkage and the glass transition of the bio-based epoxy resin system, etc. This multiscale simulation strategy can provide as a possible investigation scheme for the subsequent improvement and design of bio-based epoxy resin composite materials.

Theoretical research of covalent and controllable molecular brake based on 9-triptycene

In order to understand the mechanism of molecular brake more clearly, the brake system (3-(9-triptycyl)-6,6′-dimethoxy-2,2′-bipyridine) was studied in computational methods using the density functional theory (DFT). The M06-2X functional is used to obtain various parameters of the molecules. The relaxed potential energy surface scans were performed to obtain the minimum energy profiles (MEPs). The ground state and transition state during rotation are accurately found, and then a lot of thermodynamic data are obtained and analyzed. For the purpose of proving the occurrence of rotation motion, the transition state theory (TST) was used to investigate the kinetic properties. The Boltzmann statistics was used to analyze the conformer populations, which can also explain some thermodynamic properties of molecular brake. Based on these results, the braking mechanism was pointed out: The rotation of triptycene (Tp) rotor was suppress by a chemical method, to terminate the motion completely, the temperature was lowered appropriately. The molecular dynamics (MD) simulations of the ground states and transition states were also carried out to further verify the rationality of the mechanism. Comparing with the experimental results, the conclusions were figured out.

Activation of D2 by Neodymium Cation (Nd+): Bond Energy of NdH+ and Mechanistic Insights through Experimental and Theoretical Studies.

The kinetic-energy-dependent cross section for the reaction of Nd+ with D2 was studied by using a guided ion beam tandem mass spectrometer. The formation of NdD+ is endothermic, and analysis of the reaction cross section gave an NdH+ 0 K bond dissociation energy (BDE) of 1.99 ± 0.06 eV. Theoretical calculations for the NdH+ BDE were performed for comparison with the experimental thermochemistry and generally gave accurate results. Additionally, relaxed potential energy surfaces for NdH2+ were performed, and no strongly bound dihydride intermediate was located. The Nd+ + D2 reactivity and BDE of NdH+ are compared with analogous results for the lanthanide cations La+, Ce+, Pr+, Sm+, Gd+, and Lu+ to establish periodic trends and insight into the role of the electronic configurations on this reactivity and the lanthanide hydride cation bond strengths.

Structural and theoretical analysis of 2-chloro-4-nitroaniline and 2-methyl-6-nitroaniline salts.

The crystal structures of five new salts of 2-chloro-4-nitroaniline (2Cl4na) and 2-methyl-6-nitroaniline (2m6na) with inorganic acids, namely, 2-chloro-4-nitroanilinium bromide, C6H6ClN2O2+·Br- (1), 2-chloro-4-nitroanilinium hydrogen sulfate, C6H6ClN2O2+·HSO4- (2), 2-methyl-6-nitroanilinium bromide, C7H9N2O2+·Br- (3), 2-methyl-6-nitroanilinium triiodide, C7H9N2O2+·I3- (4), and 2-methyl-6-nitroanilinium hydrogen sulfate, C7H9N2O2+·HSO4- (5), were determined by single-crystal X-ray diffraction. Theoretical calculations of the relaxed potential energy surface (rPES) revealed that the energy barriers for the rotation of the nitro group for isolated H2Cl4na+ and H2m6na+ cations are 4.6 and 11.6 kcal mol-1, respectively. The ammonium group and respective anions form hydrogen bonds which are the most important interactions and are arranged in zero- (in 3), one- (in 1 and 4) or two-dimensional (in 2 and 5) networks. Hydrogen-bonding patterns were analyzed by means of mathematical relationships between graph-set descriptors and compared with previously reported nitroaniline salts. Hirshfeld surface analysis indicates that the nitro group plays a dominant role among the weak interactions, i.e. C-H...O(NO2), NO2...π(Ar) and O(NO2)...π(NO2). The frequency of the νsNO2 vibration is correlated with the type of interaction in which the NO2 group is involved. Analysis of the νsNO2 band observed in the IR and Raman spectra allowed an assessment of its shift in the sequence (H2m6na)I3 (4) < (H2m6na)HSO4 (5) < (H2m6na)Br (3) < (H2Cl4na)Br (1) < (H2Cl4na)HSO4 (2).

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP.

Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2′-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1′-β-D-2′- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S0 and S1 states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S1 state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S0 and S1 states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S1 state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.