Vibrational Frequency Shifts Research Articles

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates.

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2-H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H2-H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

A computational study of hydrogen-bonded X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) complexes

An MP2/6-311++G(3df,3pd) computational study of a series of hydrogen-bonded complexes X3CH⋯YZ (X = Cl, F, NC; YZ = FLi, BF, CO, N2) was undertaken to assess the trends in the relative stability and other molecular properties with variation of both the X group and the chemical hardness of the Y atom of YZ. The red- and blue-shifting propensities of the proton donor X3CH were investigated by considering the CH bond length change and its associated vibrational frequency shift. The proton donor Cl3CH, which has a positive dipole moment derivative with respect to CH bond extension, tends to form red-shifted complexes, this tendency being modified by the hardness (and dipole moment) associated with the proton acceptor. On the other hand, F3CH has a negative dipole moment derivative and tends to form blue-shifted complexes, suggesting that as X becomes more electron-withdrawing, the proton donor should have a negative dipole moment derivative and form blue-shifted complexes. Surprisingly, the most polar proton donor (NC)3CH was found to have a positive dipole moment derivative and produces red-shifted complexes. A perturbative model was found useful in rationalizing the trends for the CH bond length change and associated frequency shift.

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles.

We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional theory that includes Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum.

Computational investigation of CO adsorbed on Aux, Agx and (AuAg)x nanoclusters (x = 1 \u2212 5, 147) and monometallic Au and Ag low-energy surfaces

Density functional theory calculations have been performed to investigate the use of CO as a probe molecule for the determination of the structure and composition of Au, Ag and AuAg nanoparticles. For very small nanoclusters (x = 1 − 5), the CO vibrational frequencies can be directly correlated to CO adsorption strength, whereas larger 147-atom nanoparticles show a strong energetic preference for CO adsorption at a vertex position but the highest wavenumbers are for the bridge positions. We also studied CO adsorption on Au and Ag (100) and (111) surfaces, for a 1 monolayer coverage, which proves to be energetically favourable on atop only and bridge positions for Au (100) and atop for Ag (100); vibrational frequencies of the CO molecules red-shift to lower wavenumbers as a result of increased metal coordination. We conclude that CO vibrational frequencies cannot be solely relied upon in order to obtain accurate compositional analysis, but we do propose that elemental rearrangement in the core@shell nanoclusters, from Ag@Au (or Au@Ag) to an alloy, would result in a shift in the CO vibrational frequencies that indicate changes in the surface composition.

(H, Li)Br and LiOH Solvation Bonding Dynamics: Molecular Nonbond Interactions and Solute Extraordinary Capabilities.

We resolved the O:H-O bond transition from the mode of ordinary water to its hydration in terms of its phonon stiffness (vibration frequency shift Δω), order of fluctuation (line width), and number fraction (phonon abundance), fx(C) = Nhyd/Ntotal. The fx(C) follows fH(C) = 0, fLi(C) ∝ fOH(C) ∝ C, and fBr(C) ∝ 1 - exp(-C/C0) toward saturation with C being the solute concentration. The invariant dfx(C)/dC suggests that the solute forms a constantly sized hydration droplet without responding to interference of other ions because its hydrating H2O dipoles fully screen its electric field. However, the number inadequacy of the highly ordered hydration H2O dipoles partially screens the large Br-. The Br- then interacts repulsively with other Br- anions, which weakens its electric field and the fBr(C) approaches saturation at higher solute concentration. The consistency in the concentration trend of the fLiBr(C), the Jones-Dole viscosity η(C), and the surface stress of LiBr solution clarifies their common origin of ionic polarization. The resultant energy of the solvent H-O exothermic elongation by O: ⇔ :O repulsion and the solute H-O endothermic contraction by bond-order deficiency heats up the LiOH solution. An estimation of at least 0.15 eV (160% of the O:H cohesive energy of 0.1 eV) suggests that the H-O elongation is the main source heating up the solution, while the molecular motion, structure fluctuation, or even evaporation dissipates energy caped at 0.1 eV.

A theoretical study of the confinement effects on the energetics and vibrational properties of 4,4'-bipyridine adsorption on H-ZSM-5 zeolite.

The confinement effects of a zeolite framework on the adsorption of a bidentate 4,4'-bipyridine (44BPY) ligand on the straight channel of H-ZSM-5 have been investigated by density functional theory calculations using B3LYP, B3LYP-D3, M06-2X, M06-2X-D3 functionals, and the MP2 method with two basis sets 6-31+G* and 6-31++G(2d,2p). The straight channel is simulated by a realistic cluster model of 32 tetrahedra (T), having two aluminum atoms located in the straight and intersection regions, respectively. The potential energy surface of the double proton transfer reaction from the Brønsted acid sites of H-ZSM-5 to 44BPY is characterized by three minima corresponding to two monodentate ion pair complexes 44BPYH+/32T- and one bidentate ion pair complex 44BPYH22+/32T2- formed consecutively via two distinct pathways. No energy minimum is found for a neutral hydrogen bonding structure. The relative stabilities of these 44BPY adsorption complexes and the transition states connecting them do not exceed 4.9 and 4.2 kcal mol-1, respectively. Consequently equilibrium between the mono and bidentate complexes could be established. Our results clearly show that the adsorption energy for all complexes is substantially governed by the confinement effects executed through steric constraints and dispersive van der Waals interactions. The calculated vibrational frequencies and frequency shifts of 44BPY adsorbed as mono or diprotonated species are in good agreement with our Raman spectra of 44BPY occluded in H-ZSM-5 of different Si/Al ratios.

Test of weak equivalence principle of microscopic particles based on atom interferometers

The equivalence principle is one of the two basic assumptions of general relativity. It is the extension of weak equivalence principle. At present, a lot of experiments have tested the weak equivalence principle within a certain accuracy. However, the new theories that unify the gravity and the standard model require the weak equivalence principle to be broken, so the highly accurate test of the weak equivalence principle has important scientific significance. The test of the weak equivalence principle using microscopic particles complements and extends that using macroscopic objects. In this paper, the principle of the atomic interferometer is introduced, and the history and status quo of experimental study on weak equivalence principle of microscopic particles using atomic interferometer are reviewed. The precision of experiments using different-mass atoms is improved from 10-7 to 10-8, the precision of experiment using different spin-orientation atoms reaches the level of 10-7, and the precision of quantum test using superposition-state atoms reaches the level of 10-9. The key problems in the weak equivalence principle test using dual-species atom interferometers are summarized. Advances have been made in vibration noise suppression, frequency shift and phase noise suppression of Raman laser, four-wave double-diffraction Raman-transition atom interference, signal detection and data processing. The development of long-baseline atom interferometers for improving the free evolution time of atoms has progressed. The precision of demonstration experiment of weak equivalence principle test using atom interferometers in weightlessness reaches 10-4 level. The space plan for atom interferometer based weak equivalence principle test is also gradually implemented. The test precision of microparticles' weak equivalence principle using long-baseline atom interferometers or space atom interferometers is expected to reach the level of 10-15-10-17 in the future.

Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation of CO in the Heme Distal Pocket of Myoglobin

Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B1 and B2 states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B1 and B2 states correspond to Fe⋯CO (with carbon atom closer to iron center of heme) and Fe⋯OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B1 and B2 is 13.1 cm−1, which is in good agreement with experimental value of 11.5 cm−1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.

Mono, di, tri and tetraethylene glycol: Spectroscopic characterization using density functional method and experiment

We report infrared and electronic absorption spectra of mono, di, tri and tetra ethylene glycol (EG) in gas phase, their cation and anion and in water solvent using density functional theory calculations at B3LYP/TZVP level. Structural paramaters, rotational and centrifugal distortional constants and dipole moments are also reported. A siginificant shifts in vibrational frequencies and peaks in electronic absorption spectra have been observed upon ionization of mono, di, tri and tetra ethylene glycols. We have also obtained experimental vibrational spectrum of monoethylene glycol. Vibrational frequencies of mono ethylene glycol from theory and experiment are compared. We have used integral equation formalism polarizable continuum model (IEFPCM) model to study the influence of water solvent on vibrational frequencies of neutral mono, di, tri and tetra ethylene glycol. Electronic absorption spectra for these molecules have been obtained using Time dependent density functional theory (TDDFT).

Electronic structure, spectral characteristics and physicochemical properties of linear, branched and cyclic alkyl group substituted 1-alkyl-3-butylimidazolium cation based ionic liquids

Room temperature ionic liquids (RTILs) composed of linear, cyclic or branched alkyl substituted 1-alkyl-3-butylimidazolium and bis{(trifluoromethyl)sulfonyl}imide (Tf2N) ion pairs have been modeled using the density functional theory. Electronic Structure, infrared and 1H NMR spectra of these ion pairs are presented. Calculated interaction energies accompanying the ion pair formation with varying alkyl substituent follows the order: isopentyl>n-pentyl>3-pentyl>cyclopentyl. The cation-anion binding in Tf2N ion pairs and those in their precursors composed of Br− ions are unraveled through the quantum theory of atoms in molecules and non-covalent interaction index reduced density gradient methods. The formation of Tf2N ion-pairs is governed by C-H⋅⋅⋅O hydrogen bonding, anion-π and electrostatic interactions from the imidazolium cation whereas the Br− ion pairs reveal dominance of the C∙∙∙Br orbital interactions. Use of natural bond orbital (NBO) analyses establish the correlation between the electron density in σ*(C-H) natural orbital and the observed decomposition temperature (Td) for the Tf2N based RTILs. Further a larger shift in vibrational frequency of the characteristic aromatic C-H stretching from the imidazolium cation in the infrared spectra suggests the lowered Td values.

An oxorhenium complex bearing a chiral cyclohexane-1-olato-2-thiolato ligand: Synthesis, stereochemistry, and theoretical study of parity violation vibrational frequency shifts.

In our effort towards measuring the parity violation energy difference between two enantiomers, a simple chiral oxorhenium complex 5 bearing enantiopure 2-mercaptocyclohexan-1-ol has been prepared as a potential candidate species. Vibrational circular dichroism revealed a chiral environment surrounding the rhenium atom, even though the rhenium is not a stereogenic center itself, and enabled to assign the (1S,2S)-(-) and (1R,2R)-(+) absolute configuration for 5. For both compound 5 and complex 4, previously studied by us and bearing a propane-2-olato-3-thiolato ligand, relativistic calculations predict parity violating vibrational frequency differences of a few hundreds of millihertz, above the expected sensitivity attainable by a molecular beam Ramsey interferometer that we are constructing.

Evaluation of non-covalent interactions of chlorambucil (monomer and dimer) and its interaction with biological targets: Vibrational frequency shift, electron density topological and automated docking analysis

Chlorambucil is a well-known chemotherapy drug that is being used to treat chronic myelogenous leukemia. As it contains ten flexible rotational bonds, the possible spatial conformations have been identified theoretically. The spectral signatures of monomer and dimer structures of chlorambucil and the frequency shifts due to non-covalent interactions (NCIs) have been illustrated using FT-IR and FT-Raman spectra. The bond correlation between carbon and hydrogen nuclei of chlorambucil has been obtained using 2D-HSQC NMR spectrum. The assignments of harmonic normal modes have been done in order to find the vibrational contributions of each functional group. Besides the spectroscopic studies, the electron density based quantum topological atoms in molecule analysis have been performed to explore the possible interactions between the non-bonded atoms. The reduced density gradient and isosurface plots have been used in this study to understand the strength of NCIs. The charge delocalization patterns of monomer and dimer structures were explained so as to investigate the chemical stability profile. The active sites for the electrophilic and nucleophilic attack on the monomer conformers have been determined by applying Hirshfeld charges and atomic spin densities into Fukui and Parr functions, respectively. From the automated docking analysis, it is found that chlorambucil interacts with the aldo-keto reductase family 1 (AKR1B1, AKR1B10, AKR1B15) and FAD-linked sulfhydryl oxidase ALR proteins through strong hydrogen bonds and shows a potential inhibition. In order to take into account the interactions ranging from short to long range, the modern density functionals viz. M06-2X, wB97XD, B97D which includes dispersion-corrected repulsion terms have been employed and the theoretical results were found coincide with the experimental observations.

On the interaction of cyanoformaldehyde with HNO, HF, HCl, H2O, and CH3OH: A preference for orthogonal structures

The potential energy surfaces of the complexes of cyanoformaldehyde, (formyl cyanide, HCOCN), with HNO, HF, HCl, H2O, and CH3OH have been investigated theoretically at the MP2 and CCSD(T) levels using several extended basis sets. Twenty-two low-lying minima have been detected, seven for HCOCN-HNO, three for each of the HCOCN-HF and HCOCN-HCl dimers, four for HCOCN-H2O and five for the HCOCN-CH3OH complex. The two most stable HCOCN-HNO complexes have non-planar structures as do the most stable arrangements of HCOCN-H2O and HCOCN-CH3OH. The vibrational frequency shifts typical for formyl groups engaged in hydrogen bonding, red shifts of CO stretches and blue shifts of CH stretches, occur in most of the dimers. Similarly, in almost all HCOCN-HNO complexes, the NH stretching frequencies are also blue-shifted. However, in case of the two most stable HCOCN-HNO complexes, red shifts of harmonic NH stretches are calculated. Inclusion of anharmonic contributions reduces these red shifts substantially and in one case converts the red shift to a blue shift. Conventional red shifts of XH (X=F, Cl, O) stretching frequencies and blue shifts for formyl CH stretches are calculated for the complexes with HF, HCl, H2O, and CH3OH.

Signatures of vibronic coupling in two-dimensional electronic-vibrational and vibrational-electronic spectroscopies.

Two-Dimensional Electronic-Vibrational (2D EV) spectroscopy and Two-Dimensional Vibrational-Electronic (2D VE) spectroscopy are new coherent four-wave mixing spectroscopies that utilize both electronically resonant and vibrationally resonant field-matter interactions to elucidate couplings between electronic and vibrational degrees of freedom. A system Hamiltonian is developed here to lay a foundation for interpreting the 2D EV and 2D VE signals that arise from a vibronically coupled molecular system in the condensed phase. A molecular system consisting of one anharmonic vibration and two electronic states is modeled. Equilibrium displacement of the vibrational coordinate and vibrational frequency shifts upon excitation to the first electronic excited state are included in our Hamiltonian through linear and quadratic vibronic coupling terms. We explicitly consider the nuclear dependence of the electronic transition dipole moment and demonstrate that these spectroscopies are sensitive to non-Condon effects. A series of simulations of 2D EV and 2D VE spectra obtained by varying parameters of the system, system-bath, and interaction Hamiltonians demonstrate that one of the following conditions must be met to observe signals: (1) non-zero linear and/or quadratic vibronic coupling in the electronic excited state, (2) vibrational-coordinate dependence of the electronic transition dipole moment, or (3) electronic-state-dependent vibrational dephasing dynamics. We explore how these vibronic interactions are manifested in the positions, amplitudes, and line shapes of the peaks in 2D EV and 2D VE spectroscopies.

Paving the Way for the Molecular-Level Design of Adsorbents for Carbon Capture: A Quantum-Chemical Investigation of the Adsorption of CO2 and N2 on Pure-Silica Chabazite

Pure-silica chabazite is a promising material for capturing CO2 from flue gases in adsorption-based carbon capture and storage. The adsorption of CO2 and N2 on pure-silica chabazite has been studied at the molecular level with Density Functional Theory in the finite cluster/supermolecule approach. Molar enthalpies of adsorption of CO2 and N2 have been calculated with excellent agreement (<1.0 kJ/mol) with the experimental values. Additionally, the experimental structural information available in the case of CO2 could be correctly reproduced and even better interpreted. Vibrational frequency shifts for both adsorbate molecules and site-specific information for the case of N2, which are not yet available from experiment, could be anticipated. The results of this work indicate that this type of analysis may pave the way for the development of a new generation of adsorbents, designed at the molecular level, for capturing CO2 from flue gases by adsorptive separation processes.

Scenarios of polaron-involved molecular adsorption on reduced TiO2(110) surfaces

The polaron introduced by the oxygen vacancy (Vo) dominates many surface adsorption processes and chemical reactions on reduced oxide surfaces. Based on IR spectra and DFT calculations of NO and CO adsorption, we gave two scenarios of polaron-involved molecular adsorption on reduced TiO2(110) surfaces. For NO adsorption, the subsurface polaron electron transfers to a Ti:3d-NO:2p hybrid orbital mainly on NO, leading to the large redshifts of vibration frequencies of NO. For CO adsorption, the polaron only transfers to a Ti:3d state of the surface Ti5c cation underneath CO, and thus only a weak shift of vibration frequency of CO was observed. These scenarios are determined by the energy-level matching between the polaron state and the LUMO of adsorbed molecules, which plays a crucial role in polaron-adsorbate interaction and related catalytic reactions on reduced oxide surfaces.

A computational investigation of the red and blue shifts in hydrogen bonded systems

The present work reports results of computational investigations of hydrogen bonding, with regard to the most common red shift in the vibrational frequency, as well as the less common blue shift in several hydrogen bonded systems. A few new correlations of the frequency shifts with the calculated electrostatic parameters are proposed, thereby generating new insight into both types of the frequency shifts. Thus, the frequency shifts in X—H—-Y hydrogen bonded systems at different H—Y distances are shown to correlate well with the Mulliken charges on H and Y, with the positive and negative charges on Y correlating with the blue and red shift of the frequency of X—H vibration, respectively. The role played by charge transfers at other parts of the interacting system is also discussed. Synopsis The blue and red shifts in vibrational frequency in X—H...Y hydrogen bonded systems as a function of H—-Y distance are shown to correlate well with the atomic charges on H and Y as well as other electrostatic parameters.

Periodic Dispersion-Corrected Approach for Isolation Spectroscopy of N2 in an Argon Environment: Clusters, Surfaces, and Matrices.

Ab initio and Perdew, Burke, and Ernzerhof (PBE) density functional theory with dispersion correction (PBE-D3) calculations are performed to study N2-Arn (n ≤ 3) complexes and N2 trapped in Ar matrix (i.e., N2@Ar). For cluster computations, we used both Møller-Plesset (MP2) and PBE-D3 methods. For N2@Ar, we used a periodic-dispersion corrected model for Ar matrix, which consists on a slab of four layers of Ar atoms. We determined the equilibrium structures and binding energies of N2 interacting with these entities. We also deduced the N2 vibrational frequency shifts caused by clustering or embedding compared to an isolated N2 molecule. Upon complexation or embedding, the vibrational frequency of N2 is slightly shifted, while its equilibrium distance remains unchanged. This is due to the weak interactions between N2 and Ar within these compounds. Our calculations show the importance of inclusion of dispersion effects for the accurate description of geometrical and spectroscopic parameters of N2 isolated, in interaction with Ar surfaces, or trapped in Ar matrices.

Guest Hydrogen Bond Dynamics and Interactions in the Metal–Organic Framework MIL-53(Al) Measured with Ultrafast Infrared Spectroscopy

MIL-53(Al) is among the most “flexible” metal–organic frameworks and significantly changes its structure when guest molecules are introduced into the framework’s pores. The guest molecules interact with μ2-OH, which is a hydroxyl group bridging two aluminums. This interaction is thought to play an important role in the adsorption of molecules into the pores. Here, we report infrared absorption, infrared pump–probe, and two-dimensional infrared spectroscopy on a deuterated bridging hydroxyl, μ2-OD, in MIL-53(Al) loaded with various guest molecules. Depending on guest, large vibrational frequency shifts, broadening of absorption band, enhancement of absorption coefficient, and acceleration of vibrational relaxation were observed, which are all signatures of hydrogen bonding interactions between the bridging hydroxyls and the guest. 2D IR spectroscopy reveals that the time evolution of the vibrational frequency occurs on multiple time scales: subpicosecond dynamics caused by localized hydrogen bond fluctuati...

Quantifying Biomolecular Recognition with Site-Specific 2D Infrared Probes

Azidohomoalanine (Aha) is an unnatural amino acid containing an infrared active azido side chain group that can, through frequency shifts of the azido stretch vibration, act as a probe of local structure. To realize the potential of such structural probes for protein science, we have developed a two-dimensional infrared spectrometer employing fast mechanical scanning and intrinsic phasing of the resulting spectra, leading to a lower sensitivity limit of ∼100 μOD level samples. Using this approach, we quantify the biomolecular recognition between a PDZ2 domain and two Aha-mutated peptides. It is shown that this method can distinguish different binding modes and that the energetics of binding can be determined.