Vibrational Transition Moment Directions Research Articles

Vibrational Cross-Angles in Condensed Molecules: A Structural Tool

The fluctuations of three-dimensional molecular conformations of a molecule in different environments play critical roles in many important chemical and biological processes. X-ray diffraction (XRD) techniques and nuclear magnetic resonance (NMR) methods are routinely applied to monitor the molecular conformations in condensed phases. However, some special requirements of the methods have prevented them from exploring many molecular phenomena at the current stage. Here, we introduce another method to resolve molecular conformations based on an ultrafast MIR/T-Hz multiple-dimensional vibrational spectroscopic technique. The model molecule (4'-methyl-2'-nitroacetanilide, MNA) is prepared in two of its crystalline forms and liquid samples. Two polarized ultrafast infrared pulses are then used to determine the cross-angles of vibrational transition moment directions by exciting one vibrational band and detecting the induced response on another vibrational band of the molecule. The vibrational cross-angles are then converted into molecular conformations with the aid of calculations. The molecular conformations determined by the method are supported by X-ray diffraction and molecular dynamics simulation results. The experimental results suggest that thermodynamic interactions with solvent molecules are not altering the molecular conformations of MNA in the solutions to control their ultimate conformations in the crystals.

Testing a new analytical approach for determination of vibrational transition moment directions in low symmetry planar molecules: 1-D- and 2-D-naphthalene

A new analytical approach for improving the precision in determination of vibrational transition moment directions of low symmetry molecules (lacking orthogonal axes) is discussed in this paper. The target molecules are partially uniaxially oriented in nematic liquid crystalline solvent and are studied by IR absorption spectroscopy using polarized light. The fundamental problem addressed is that IR linear dichroism measurements of low symmetry molecules alone cannot provide sufficient information on molecular orientation and transition moment directions. It is shown that computational prediction of these quantities can supply relevant complementary data, helping to reveal the hidden information content and achieve a more meaningful and more precise interpretation of the measured dichroic ratios.The combined experimental and theoretical/computational method proposed by us recently for determination of the average orientation of molecules with Cs symmetry has now been replaced by a more precise analytical approach. The new method introduced and discussed in full detail here uses a mathematically evaluated angle between two vibrational transition moment vectors as a reference. The discussion also deals with error analysis and estimation of uncertainties of the orientational parameters. The proposed procedure has been tested in an analysis of the infrared linear dichroism (IR–LD) spectra of 1-D- and 2-D-naphthalene complemented with DFT calculations using the scaled quantum mechanical force field (SQM FF) method.

Electronic and Vibrational Transition Moment Directions in 7-Dimethylamino-3-methyl-N-methyl-d3-4-phenylethynylcarbostyril

We report the synthesis and photophysical characterization of 7-dimethylamino-3-methyl-N-methyl-d(3)-4-phenylethynylcarbostyril, a chromophore of interest as a rotator in surface-mounted molecular rotors. Measurement of UV-vis absorption and fluorescence spectra, steady state fluorescence and excitation anisotropy, and linear dichroism in the IR and UV-vis permitted a determination of absolute vibrational and electronic transition moment directions in this previously unreported chromophore. The first singlet-singlet absorption and fluorescence are polarized perpendicular to the axle of the rotator. Density functional theory calculations of electronic excitation and vibrational frequencies gave results in very good agreement with those observed. Calculated IR transition moment directions showed rather poor agreement with experiment.

Vibrational transition moment directions of a terminally p-nitrobenzyl substituted long-chain alkanethiol by polarized infrared spectra and DFT calculations

Transition moment directions of the vibrational states of nitro and carbonyl groups of p-nitrobenzyl-16-mercaptohexadecanoate are evaluated by infrared linear dichroism (IR LD) to be further exploited as film orientation markers in self-assembled monolayers (SAMs) that the respective compound forms on metal surfaces. DFT calculations followed by a complete normal coordinate analysis were employed to assist in the vibrational bands assignments. The analysis of the experimental IR LD spectra in conjunction with the step-wise reduction procedure of Thulstrup–Eggers indicated that the transition moment directions of the antisymmetric NO 2 stretching and the carbonyl stretching modes are collinear, and confirmed previous results that those of the symmetric and the antisymmetric NO 2 stretching vibrations are not exactly mutually perpendicular.

Infrared linear dichroism in stretched films: Quantum mechanical approach within the polarizable continuum model

AbstractIn this work we discuss how environmental effects on vibrational transition moment directions for molecules dispersed in stretched films can be accounted for via the integral equation formalism polarizable continuum model (IEFPCM). In particular, effects related to the matrix polarization induced by the probing field (cavity field terms) are taken into account. Calculations are performed for three DNA‐related molecules (9‐methyladenine, 7‐methyladenine, and 2‐amino‐9‐methylpurine) for which infrared linear dichroism (IR LD) has been measured experimentally. By combining experimental data and calculations, different parameters of the film (Saupe order parameters and orientational axis direction) can be obtained and used to give “experimental” estimates of transition moment directions. The results show the importance of accounting for the environment surrounding the molecule in transition moment calculations. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Chlorinated Guest Orientation and Mobility in Clathrate Structures Formed with Syndiotactic Polystyrene

Syndiotactic polystyrene films uniaxially stretched at different draw ratios, and including different crystalline (δ and γ) phases as well as clathrate phases with 1,2-dichloropropane, 1,2-dichloroethane, and 1-chloropropane, have been studied by combined infrared linear dichroism and X-ray diffraction measurements. Information relative to the orientation and mobility of trans and gauche conformers of these chlorinated guests in their clathrate structures with syndiotactic polystyrene has been achieved by comparison between experimentally evaluated and calculated vibrational transition moment directions of conformationally sensitive infrared peaks of the guest molecules.

Vibrational polarization spectroscopy of fluorene: alignment in stretched polymers and nematic liquid crystals

New linear dichroism spectra in the mid-IR region of fluorene aligned in stretched polymers and nematic liquid crystals are compared with earlier experimental and theoretical investigations. Linear dichroism spectra of molecules aligned in such anisotropic solvents are simple to obtain, especially for small and medium sized molecules. Most molecules obtain a satisfactory alignment by these methods and the spectra are simple to interpret.The information obtained from these spectra about vibrational transition moment directions is often crucial for vibrational assignments in molecules like fluorene. Even high quality calculations are still unable to provide safe assignments for all fundamentals in fluorene as long as they are only compared with traditional spectra. Linear dichroism spectra provide a separation of the experimental information according to symmetry classes (particularly striking for molecules of C2v and similar symmetries); this reduces the assignment puzzle drastically. In the present case the result is an almost complete and safe assignment of all symmetry allowed invibrational fundamentals of fluorene. A number of earlier assignments, which had been questioned or were doubtful, have been confirmed or corrected.

Molecular and vibrational structure of 2,2′-dihydroxybenzophenone: infrared linear dichroism and quantum chemical calculations

The molecular vibrations of the title compound (DHBP) were investigated by IR polarization spectroscopy on samples partially aligned in stretched polyethylene (PE) and correlated with those of the closely related compound anthralin (1,8-dihydroxy-9(10H)-anthracenone). Compared to the case of anthralin, the analysis of the observed linear dichroism (LD) for DHBP is complicated by lower molecular symmetry and by less efficient alignment in stretched PE, but approximate vibrational transition moment directions could be derived for about 27 vibrational transitions. The molecular geometry and normal vibrational modes were calculated by ab initio Hartree–Fock (HF) theory and by various density functional theories (DFT). As in the case of anthralin, vibrational motions associated with the carbonyl and hydroxy groups couple strongly with CC and CH motions, resulting in the prediction of a very complex IR spectrum. Excellent consistency with observed transitions was obtained with DFT, particularly with the B3LYP functional, while corresponding HF results were much less satisfactory, partly because of failure to describe the intramolecular H-bonding prevailing in DHBP.

A Density Functional, Infrared Linear Dichroism, and Normal Coordinate Study of Phenol and its Deuterated Derivatives: Revised Interpretation of the Vibrational Spectra

The assignment of the vibrational spectra of phenol has been reexamined on the basis of Raman and new IR measurements and theoretical analysis of the normal modes of vibrations in the electronic ground state. The infrared spectra of C6H5OH, C6D5OD, and C6D5OH have been studied in solution and vapor phases, as well as has the Raman spectra in solutions. New experimental data were obtained from infrared linear dichroism (IR-LD) studies of phenol aligned in uniaxially oriented nematic liquid crystal solution. The measured dichroic ratios and orientation factors indicate an effective Cs symmetry of the molecule with coplanar orientation of OH bond with the benzene ring and supply unique information on the extent of symmetry lowering of benzene normal modes. The fundamental vibrational frequencies, force constants, and dipole derivatives have been calculated by ab initio quantum chemical methods applying the B3P86 density functional approximation with 6-311G** basis set. The force field optimized by means of a least-squares scaling procedure for phenol-d0 (using six scale factors) was used to calculate the frequencies (with a mean deviation from the observed values less than 1%), normal modes, potential energy distributions, transition moment vectors, and IR intensities for phenol-d0, -d1, -d5, and -d6 isotopomers. Compared to the deviations between the calculated and observed absorption intensities, a more satisfactory correlation was found between the calculated and experimentally determined vibrational transition moment directions. The results indicate unanimously that the perturbation of the normal modes of benzene by the asymmetric hydroxyl substituent is so great that the previous practice of assigning the normal vibrations of phenol to those of benzene or even to C2v symmetry species is not justified.

Vibrational Transition Moments of Aminopurines: Stretched Film IR Linear Dichroism Measurements and DFT Calculations

Vibrational transition moment directions for 7-methyladenine (7MA), 9-methyladenine (9MA), and 2-amino-9-methylpurine (2A9MP) have been determined from infrared linear dichroism measurements on samples partially oriented in stretched poly(vinyl alcohol) (PVA) films. The sign ambiguity problem for the experimental directions of 9MA and 2A9MP was in part solved by exploiting the change in orientation character of the ribose derivatives adenosine and 2-aminopurine riboside. In the case of all transitions in 7MA and most transitions in 9MA and 2A9MP, polarizations calculated in self-consistent-reaction-field (SCRF) DFT(B3LYP)/6-31G(d,p) calculations were used to guide the choice of experimental polarizations. The SCRF spectra were generally in better agreement with experiment than the corresponding calculated gas-phase spectra. The IR spectrum of adenine in PVA film was analyzed in terms of contributions from the 7-H and 9-H tautomers, and the relative abundance of the minor 7-H tautomer in PVA film was determined to be 23 ± 3% at room temperature.

IR Transition Moments of 1,3-Dimethyluracil: Linear Dichroism Measurements and ab Initio Calculations

The vibrational transition moment directions of 1,3-dimethyluracil (DMU), 1,3-dimethyluracil-5-d (DMU-5-d), and 1,3-dimethyluracil-6-d (DMU-6-d) have been determined from measurements of polarized IR spectra on samples partially aligned in stretched poly(vinyl alcohol) and by ab initio calculations at the HF/6-31G* level of approximation. The agreement between experiments and theory is good. IR spectra of DMU, DMU-5-d, and DMU-6-d in KBr and in D2O form, together with the calculated spectra and the IR polarizations, the basis for some reassignments. Special attention is paid to the double-bond region, where the high-frequency carbonyl stretching mode is assigned to an in-phase vibration of the C4O and the C2O. This vibration is polarized in a direction almost bisecting the angle between the two carbonyl bonds, in agreement with an in-phase assignment. The low-frequency mode is the out-of-phase vibration of the two carbonyl groups, and it is consequently polarized perpendicular to the high-frequency mode. In order to determine the orientation axis of DMU in the polymer matrix, the UV linear dichroism (LD) spectrum was measured and the polarizations of the electronic transitions were estimated from a semiempirical self-consistent reaction field (SCRF) calculation including solvent effects. The combined information from IR LD and UV LD shows that the molecular orientation axis in the stretched film experiment is parallel to the first pi --> pi* transition in DMU.

IR polarization directions in s-trans-1,3-butadiene and the average topochemistry of the s-cis to s-trans photoisomerization in matrix isolation

Vibrational transition moment directions of s-trans-1,3-butadiene were deduced from measurements of its IR linear dichroism on samples partially oriented (i) by photoselective photoiosomerization of s-cis-1,3-butadiene isolated in inert-gas matrices with linearly polarized light, (ii) in stretched polyethylene, and (iii) in stretched poly(ethylene-d 4 ). The moment directions are in quite good agreement with those predicted by theory at the MP2/6-311G** level of approximation. For two plausible mechanisms of s-cis to s-trans isomerization, it predicts the observed near coincidence of the C 1 -C 4 directions. For another reaction path, it predicts a 30 o angle between them. However, at present, it is unknown whether matrix photoisomerizations indeed proceed without exertion of a net torque on the environment

A low-cost method for the determination of vibrational transition moment directions

A simple and inexpensive method for determination of vibrational transition moment directions in infrared spectroscopy is presented. The technique is based on the alignment of molecules in squeezed polyethylene sheets and the spectra are recorded with natural light. In many cases the method is able to provide information essential for vibrational assignments. To illustrate the technique, a study of the IR spectrum of anthracene is carried out.

Vibrational transition moment directions in medium-size molecules: Experiment and theory

Linear dichroism is observed in the infrared spectra of dimethyl ether, isobutene, 2-butyne, and n-butane dissolved in stretched sheets of ordinary and perdeuterated poly-ethylene. For each observed vibrational band the orientation factor has been determined and related to the transition-moment direction for the vibration, providing information on its symmetry species. For n-butane, the angles of the vibrational transition moment directions in the molecular framework have been derived and compared with the angles calculated at various levels of semiempirical and ab initio theory.