Weakly bound clusters of biological interest

Weakly Bound Complexes of γ-Butyrolactone with Water as Observed in Matrix Isolation FTIR and Theoretical Calculations

A computational and spectroscopic analysis of weakly bound complexes of 1:1 γ-butyrolactone with water has been completed. In this work, multiple density-functional theories and perturbation theory were used to explore the energy-landscape of the complex. Four unique structures were identified in this analysis. One structure was characterized by the formation of a water to carbonyl hydrogen bond and the other three were formed from water to ester hydrogen bonds. The carbonyl-bound conformation was found to be the global minimum across a comprehensive panel of calculations. A wave function analysis demonstrated that the structures were additionally stabilized by weak van der Waals interactions. FTIR spectroscopy of matrix-isolated samples indicated the presence of at least two of the calculated geometries. The structures were identified to be a carbonyl-bound and at least one ester-bound structure. The transitions identified for the carbonyl-bound complex were noted to be significantly more intense than those of the ester bound, indicating greater prevalence in the matrix.

Molecular Structure of Salicylic Acid and Its Hydrates: A Rotational Spectroscopy Study

We present a study of salicylic acid and its hydrates, with up to four water molecules, done by employing chirped-pulse Fourier transform microwave spectroscopy. We employed the spectral data set of the parent, 13C, and 2H isotopologues to determine the molecular structure and characterize the intra- and intermolecular interactions of salicylic acid and its monohydrate. Complementary theoretical calculations were done to support the analysis of the experimental results. For the monomer, we analyzed structural properties, such as the angular-group-induced bond alternation (AGIBA) effect. In the microsolvates, we analyzed their main structural features dominated by the interaction of water with the carboxylic acid group. This work contributes to seeding information on how water molecules accumulate around this group. Moreover, we discussed the role of cooperative effects further stabilizing the observed inter- and intramolecular hydrogen bond interactions.

Characterizing the n→π* interaction of pyridine with small ketones: a rotational study of pyridine⋯acetone and pyridine⋯2-butanone

Complexes formed by pyridine and small ketones such as acetone and 2-butanone have been generated in a supersonic jet and characterized by broadband Fourier transform microwave spectroscopy combined with high-level theoretical computations. The spectra of the complexes show a quadrupole coupling hyperfine structure due to the presence of a nitrogen atom and the splittings owing to the low barriers of the internal rotation of the methyl groups bonded to the carbonyl group. The corresponding barriers have been determined from the analysis of the spectra. We show in both complexes that pyridine closes a cycle with a ketone carbonyl group through an N⋯CO n→π* tetrel interaction and a C-H⋯O contact. The n→π* tetrel bond involves the pyridine N atom lone pair and the ketone carbonyl group with a geometry approaching the Bürgi-Dunitz trajectory for the nucleophilic attack to a carbonyl group.

The CON−H…+NH2 Blue-Shifting H-Bond Stabilizing Effect on Z Secondary Amides and Cyclic System Conformational Rearrangement through an Alkylamine-Chain Migration Pathway

The paper is focusing on the amide linkage exceptional properties and usage of chemistry (conformational rearrangement, geometrical stereoisomers, spectroscopic blue shift phenomenon, protonation and deprotonation reactions, synthetic scope, and mechanistic implications). Hydrogen-bond-stabilized acylation reactions of a diamine with thioamides or nitriles reveal how substituents influence both the outcome of stereoselectivity and interactions. Inferring the chemical mechanism from the structures of reactants is dissimilar to the appropriate E isomers, the Z form becomes more favored in the secondary amides obtained. One conclusion from the estimation of Z structures, based on the 1H-15N 2D NMR spectra in comparison with the references, is the existence of the intramolecular, blue shifting CON−H…+NH2CH3 hydrogen bonds. The rearrangement of a methylamino residue provided the free base stabilized in the CH3N−H…O=CNH after deprotonation. An essential part of the publication describes systems in a highly stereoselective fashion, so the stereochemical outcome of the product is predictable now.

The structure of isolated thalidomide as reference for its chirality-dependent biological activity: a laser-ablation rotational study

Thalidomide is a drug that presents two enantiomers with markedly different pharmacological and toxicological activities. It is sadly famous due to its teratogenic effects mostly caused by the preferential docking of the (S)-enantiomer to the target protein cereblon (CRBN). To compare the structure of the bound CRBN thalidomide enantiomers with that of the isolated molecule, the rotational spectrum of laser-ablated thalidomide has been studied by chirp-pulsed Fourier transform microwave spectroscopy in supersonic jets complemented by theoretical computations. A new setup of the laser ablation nozzle used is presented. Two stable equatorial and axial conformers of thalidomide have been predicted corresponding to the two possible bent conformations exhibited by the glutarimide moiety. Only the most stable equatorial conformer has been detected. The comparison of its structure with those of the (S)- and (R)-enantiomers bound to CBRN shows that the bound (S) species is only slightly distorted. On the contrary, the bound (R)-enantiomer exhibits a highly distorted structure which affects the degree of puckering of the glutarimide ring and especially to the orientation of the phtalimide and glutarimide subunits. This is consistent with a less stable (R)-enantiomer and the known preference of (S)-thalidomide to bind CRBN, which starts the process leading to teratogenic effects.

Unravelling molecular interactions in uracil clusters by XPS measurements assisted by ab initio and tight-binding simulations

The C, N and O 1s XPS spectra of uracil clusters in the gas phase have been measured. A new bottom-up approach, which relies on computational simulations starting from the crystallographic structure of uracil, has been adopted to interpret the measured spectra. This approach sheds light on the different molecular interactions (H-bond, π-stacking, dispersion interactions) at work in the cluster and provides a good understanding of the observed XPS chemical shifts with respect to the isolated molecule in terms of intramolecular and intermolecular screening occurring after the core–hole ionization. The proposed bottom-up approach, reasonably expensive in terms of computational resources, has been validated by finite-temperature molecular dynamics simulations of clusters composed of up to fifty molecules.

Comparison of the Quenching Effects of Two Main Components of Ziziphi Spinosae Semen on Serum Albumin Fluorescence

Swertisin (6-glucosyl flavonoid) and spinosin (2″-β-O-glucopyranosyl swertisin) are two main components from Ziziphi Spinosae Semen, with anti-anxiety and hypnosis effects. The paper aims to compare the differences between the two compounds binding with serum albumins (BSA and HSA). Swertisin and spinosin statically quench intrinsic fluorescence of serum proteins by binding to proteins to form complexes. The fluorescence quenching rates of BSA induced by swertisin or spinosin are faster than those of HSA resulted by swertisin or spinosin, respectively. Each serum protein has only one binding site respectively accessible to the two compounds. Hydrophobic force and hydrogen bond play the important roles during the biding process of swertisin with proteins, but van der Waals force and hydrogen bond are major driving forces for spinosin binding to proteins. Synchronous fluorescence data show that spinosin binds to BSA and HSA and thus changes Tyr and Trp residue microenvironments, and has a greater effect on the latter. Compared with swertisin, spinosin has a stronger effect on the α-helix of proteins. But the distance between swertisin and proteins is slightly closer than spinosin. These findings will contribute to further understand the reaction of Ziziphi Spinosae Semen in the liver phase I oxidation, intestinal hydrolysis and deparaffin metabolism.

Pragmatic Many-Body Approach for Economic MP2 Energy Estimation of Molecular Clusters

We propose a procedure, within the many-body analysis (MBA) framework, for an economic yet accurate estimation of the correlated method-based energies of large molecular clusters employing Dunning's augmented basis sets. The basis of the procedure is to segregate the Hartree-Fock ( E_HF) and correlation energy ( E_C) estimations. E_HF is found to differ by tens of millihartrees (mH) from its full-calculation (FC) counterpart on truncating the MBA expansion at the two-body (MBA-2) level. On the contrary, E_C is estimated with smaller error on modest hardware with limited computation time at the (MBA-2) level. In view of this, we adopt a pragmatic method wherein the E_HF (accurate to five decimal places) is taken from the FC, whereas E_C is estimated at the MBA-2 level. This method is applied to a variety of medium to large molecular clusters at the MP2 level. Preliminary results at the CCSD(T) level for (H₂O)₁₆ and (H₂O)₁₇ are also reported with tremendous savings in wall-clock time and resources. The typical errors in MP2 and CCSD(T) energies per monomer are up to 0.1 and 0.2 mH, respectively. Thus the present method, balancing accuracy and computational economy, opens a way for estimating energies of large molecular clusters using correlated theories with large basis sets.

Pyridine–acetaldehyde, a molecular balance to explore the n→π*interaction

Weak n→π*and C–H⋯O interactions determine the structure of pyridine–acetaldehyde adduct. The n→π*distance oscillates with the methyl group internal rotation which acts as a sort of molecular balance to explore the n→π*interaction energy.

UV-Vis, Fluorescence, and Resonance Raman Spectroscopic and Density Functional Theoretical Studies on 3-Amino-1,2,4-triazole: Microsolvation and Solvent-Dependent Nonadiabatic Excited State Decay in Solution

The microsolvation and photophysics of 3-amino-1,2,4-triazole (3AT) after excitation to the light-absorbing S₂(nπ*) state were studied by using resonance Raman spectroscopy and single component artificial force-induced reaction (SC-AFIR) in a global reaction route mapping (GRRM) strategy. The vibrational spectra were assigned on the basis of experimental data and density functional theory (DFT) calculations. The resonance Raman spectra of 3AT were measured to probe the excited state structural dynamics in the Franck-Condon region. The conformations of 3AT(CH₃CN)₁, 3AT(CH₃OH)₂, and 3AT(H₂O)₂ clusters were determined by combining vibrational spectrum experiments and B3LYP/6-311++G(d,p) computations. DFT calculations were carried out to obtain the minimal excitation energies of the lower-lying singlet excited states, and the curve-crossing points. It was revealed that the short-time structural dynamics of 3AT were dominated by the N-N stretching coordinates. An excited state decay mechanism is proposed: 3AT is initially excited to the S₂(nπ*) state, then the conical intersection (CI) of the S₂(nπ*)/S₁(ππ*) potential energy surfaces is crossed, and 3AT then decays to the lower solvent-dependent excited state S₁(ππ*). It subsequently returns to the S₀ state, accompanied by a large Stokes fluorescence shift, which was interpreted as the stabilized S₁(ππ*) excited state bonding to several water molecules via intermolecular hydrogen bonding.

Hydrogen bonding and dominant conformations of hydrated sugar analogue complexes using tetrahydrofurfuryl alcohol as the model sugar molecule

Water molecules, which serve as both hydrogen bond donors and acceptors, have been found to influence the conformational landscape of gas-phase phenyl-β-d-glucopyranoside.

Structure and Dynamics in Formamide-(H2O)3: A Water Pentamer Analogue

Water self-association dominates the formation of microsolvated molecular clusters which may give rise to complex structures resembling those of pure water clusters. We present a rotational study of the complex formamide-(H₂O)₃ formed in a supersonic jet and several monosubstituted isotopologues. Formamide and water molecules form a four-body sequential cycle through N-H···O, O-H···O, and O-H···O═C hydrogen bonds, resulting in a chiral structure with a nonplanar skeleton that can be overlapped to that of water pentamer. The analysis of the ¹⁴N-nucleus quadrupole coupling effects shows the depletion of the electron density of the N atom lone pair with respect to the bare formamide that affects the amide group C-N and C═O distances. The study of the observed tunneling doublets shows that formamide-(H₂O)₃ follows a path to invert its structure driven by the flipping of water subunits and passing through successive nonplanar configurations, a motion reminiscent of the pseudorotation of water pentamer.

Vibrational spectroscopy of the mass-selected tetrahydrofurfuryl alcohol monomers and its dimers in gas phase using IR depletion and VUV single photon ionization

Tetrahydrofurfuryl alcohol (THFA, C₅H₁₀O₂) is a close chemical analog of the sugar rings present in the phosphate-deoxyribose backbone structure of the nucleic acids. In present report, the infrared (IR) spectra of the size-selected THFA monomer and its dimer have been investigated in a pulsed supersonic jet using infrared-vacuum ultraviolet (VUV) ionization. Herein, the laser light at 118nm wavelength served as the source of "soft" ionization in a time-of-flight mass spectrometer. The IR features for the monomers located at 3622cm^-1 can be assigned to the intramolecular hydrogen bonding stretch vibrations mainly referring to A and C conformers. Compared with the monomer, however, characteristic peaks for the dimer centered at 3415 and 3453cm^-1, red shifted 207 and 169cm^-1, respectively, were associated with the intermolecular hydrogen bonding stretch vibrations. Combined with the quantum-chemical calculations, the dimer in the gas phase preferred cyclic AC conformer stabled by forming two strong intermolecular hydrogen bonds, which shown the high hydrogen bond selectivity in the cluster. The conclusions drawn from the role played in the conformational flexibility by the hydroxyl and ether groups may be extended to other biomolecules.

Second-order NLO responses of two-cavity inorganic electrides Lin@B20H26 (n = 1, 2): evolutions with increasing excess electron number and various B-B connection sites of B20H26

Confining excess electrons in a specific space is an effective strategy to design nonlinear optical (NLO) molecules. The complexants with excess electrons are usually organic compounds, but these compounds are thermally unstable and thus hardly meet the processing requirements of NLO materials. To obtain better thermostability and NLO response molecules, in this work, inorganic compounds of B₂₀H₂₆ isomers containing two cavities were proposed. With the two included cavities, B₂₀H₂₆ can be doped by one or two Li atoms to form electrides of Li@B₂₀H₂₆ and Li₂@B₂₀H₂₆. These electrides show larger NLO responses, with respect to the corresponding undoped complexant of B₂₀H₂₆. Particularly, Li₂@B₂₀H₂₆ has the largest β₀ value of 108 846 a.u. (MP2/6-31+G(d) level) that is 850 times as large as that of corresponding B₂₀H₂₆. Moreover, the change of β₀ values with excess electron number is remarkable for two of the isomers, and differences between the β₀ values among those isomers are also significant owing to various B-B connection sites between the two cavities. Therefore, the present inorganic electrides have not only better performance due to the magnitude of their β₀ values but also better behavior on the molecular-level modulation of NLO.

Estimation of Ground-State and Singlet Excited-State Dipole Moments of Substituted Schiff Bases Containing Oxazolidin-2-one Moiety through Solvatochromic Methods

Absorption and fluorescence studies on novel Schiff bases (E)-4-(4-(4-nitro benzylideneamino)benzyl)oxazolidin-2-one (NBOA) and (E)-4-(4-(4-chlorobenzylidene amino)benzyl)oxazolidin-2-one (CBOA) were recorded in a series of twelve solvents upon increasing polarity at room temperature. Large Stokes shift indicates bathochromic fluorescence band for both the molecules. The photoluminescence properties of Schiff bases containing electron withdrawing and donating substituents were analyzed. Intramolecular charge transfer behavior can be studied based on the influence of different substituents in Schiff bases. Changes in position and intensity of absorption and fluorescence spectra are responsible for the stabilization of singlet excited-states of Schiff base molecules with different substituents, in polar solvents. This is attributed to the Intramolecular charge transfer (ICT) mechanism. In case of electron donating (-Cl) substituent, ICT contributes largely to positive solvatochromism when compared to electron withdrawing (-NO₂) substituent. Ground-state and singlet excited-state dipole moments of NBOA and CBOA were calculated experimentally using solvent polarity function approaches given by Lippert-Mataga, Bakhshiev, Kawskii-Chamma-Viallet and Reichardt. Due to considerable π- electron density redistribution, singlet excited-state dipole moment was found to be greater than ground-state dipole moment. Ground-state dipole moment value which was determined by quantum chemical method was used to estimate excited-state dipole moment using solvatochromic correlations. Kamlet-Abboud-Taft and Catalan multiple linear regression approaches were used to study non-specific solute-solvent interaction and hydrogen bonding interactions in detail. Optimized geometry and HOMO-LUMO energies of NBOA and CBOA have been determined by DFT and TD-DFT/PCM (B3LYP/6-311G (d, p)). Mulliken charges and molecular electrostatic potential have also been evaluated from DFT calculations.

The onset of electron-induced proton-transfer in hydrated azabenzene cluster anions

The prospect that protons from water may be transferred to N-heterocyclic molecules due to the presence of an excess electron is studied in hydrated azabenzene cluster anions using spectroscopy and computational chemistry.

Infrared spectra of small anionic water clusters from density functional theory and wavefunction theory calculations

We performed systematic theoretical studies on small anionic water/deuterated water clusters W/D(-)(N=2-6) at both density functional theory (B3LYP) and wavefunction theory (MP2) levels. The focus of the study is to examine the convergence of calculated infrared (IR) spectra with respect to the increasing number of diffuse functions. It is found that at the MP2 level for larger clusters (n = 4-6), only one extra diffuse function is needed to obtain the converged relative IR intensities, while two or three more sets of extra diffuse functions are needed for smaller clusters. Such behaviour is strongly associated with the convergence of the electronic structure of corresponding clusters at the MP2 level. It is striking to observe that at the B3LYP level, the calculated relative IR intensities for all the clusters under investigations are diverse and show no trend of convergence upon increasing the number of diffuse functions. Moreover, the increasing contribution from the extra diffuse functions to the dynamic IR dipole moment indicates that the B3LYP electronic structure also fails to converge. These results manifest that MP2 is a preferential theoretical method, as compared to the widely used B3LYP, for the IR intensity of dipole bounded electron systems.

Role of Excess Electrons in Nonlinear Optical Response

The excess electron is a kind of special anion with dispersivity, loosely bounding and with other fascinating features, which plays a pivotal role (promote to about 10(6) times in (H2O)3{e}) in the large first hyperpolarizabilities (β0) of dipole-bound electron clusters. This discovery opens a new perspective on the design of novel nonlinear optical (NLO) molecular materials for electro-optic device application. Significantly, doping alkali metal atoms in suitable complexants was proposed as an effective approach to obtain electride and alkalide molecules with excess electron and large NLO responses. The first hyperpolarizability is related to the characteristics of complexants and the excess electron binding states. Subsequently, a series of new strategies for enhancing NLO response and electronic stability of electride and alkalide molecules are exhibited by using various complexants. These strategies include not only the behaviors of pushed and pulled electron, size, shape, and number of coordination sites of complexants but also the number and spin state of excess electrons in these unusual NLO molecules.

Exploring the mechanism of isomerisation and water-migration in the water-complexes of amino-acid l-proline: electrostatic potential and vibrational analysis

This work reveals interesting pathways for water-migration and neutral ↔ zwitterionic isomerisation in the water complexes of l-proline.

Using differential mobility spectrometry to measure ion solvation: an examination of the roles of solvents and ionic structures in separating quinoline-based drugs

Understanding the mechanisms and energetics of ion solvation using differential mobility spectrometry.

Molecular tailoring approach: a route for ab initio treatment of large clusters

Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large system is broken down into two or more subsystems that can be readily treated computationally. Finally, the properties of the large system are obtained by patching the corresponding properties of all the subsystems. Due to these approximations, the resulting MTA-based energies carry some error in comparison with calculations based on the full system. An approach for correcting these errors has been attempted by grafting the error at a lower basis set onto a higher basis set. Furthermore, investigating the growth patterns and nucleation processes in clusters is necessary for understanding the structural transitions and the phenomena of magic numbers in cluster chemistry. Therefore, systematic building-up or the introduction of stochastics for generating molecular assemblies is the most crucial step for studying large clusters. In this Account, we discuss the working principle of MTA for probing molecular clusters at ab initio level followed by a brief summary of an automated and electrostatics-guided algorithm for building molecular assemblies. The molecular aggregates presented here as test cases are generated based on either an electrostatic criterion or the basin hopping method. At MP2 level computation, the errors in MTA-based grafted energies are typically reduced to a submillihartree level, reflecting the potential of finding accurate energies of molecular clusters much more quickly. In summary, MTA provides a platform for effectively studying large molecular clusters at ab initio level of theory using minimal computer hardware.

Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers

This review highlights the effects of explicit water molecules on the structures of amino acids and dipeptides, focusing on the relative stability of canonical vs. zwitterionic conformers.