Density functional study on the circular dichroism of photoelectron angular distribution from chiral derivatives of oxirane

The linear combination of atomic orbitals B-spline density functional method has been successfully applied to a series of four chiral derivatives of oxirane, to calculate the photoionization dynamical parameters, the circular dichroism in the angular distribution effect, and to identify trends along the series. The computational algorithm has proven numerically stable and computationally competitive. The photoionization cross section, asymmetry, and dichroic parameter profiles relative to valence orbitals have been systematically studied for the states which retain their nature along the series: the identified trends have been ascribed to the different electronic properties of the substituents. A rather unexpected sensitivity of the dichroic parameter to changes in the electronic structure has been found in many instances, making this dynamical property suitable to investigate the electronic structure of chiral compounds. The magnitude of the circular dichroism in the angular distribution effect does not seem to be associated with the initial state chirality, but rather to be governed by the ability of the delocalized photoelectron wave function to probe the asymmetry of the molecular effective potential.     

Direct Time‐Domain Observation of Conformational Relaxation in Gas‐Phase Cold Collisions

Cooling molecules in the gas phase is important for precision spectroscopy, cold molecule physics, and physical chemistry. Measurements of conformational relaxation cross sections shed important light on potential energy surfaces and energy flow within a molecule. However, gas‐phase conformational cooling has not been previously observed directly. In this work, we directly observe conformational dynamics of 1,2‐propanediol in cold (6 K) collisions with atomic helium using microwave spectroscopy and buffer‐gas cooling. Precise knowledge and control of the collisional environment in the buffer‐gas allows us to measure the absolute collision cross‐section for conformational relaxation. Several conformers of 1,2‐propanediol are investigated and found to have relaxation cross‐sections with He ranging from σ=4.7(3.0)×10^?18 cm² to σ>5×10^?16 cm². Our method is applicable to a broad class of molecules and could be used to provide information about the potential energy surfaces of previously uninvestigated molecules.     

Time dependent density functional study of the photoionization dynamics of SF6

The B-spline linear combination of atomic orbitals method has been employed to study the valence and core photoionization dynamics of SF6. The cross section and asymmetry parameter profiles calculated at the time dependent density functional theory level have been found to be in fairly nice agreement with the experimental data, with the quality of the exchange-correlation statistical average of orbital potential results superior to the Van Leeuwen-Baerends 94 (LB94) ones [Phys. Rev. A 49, 2421 (1994)]. The role of response effects has been identified by a comparison of the time dependent density functional theory results with the Kohn-Sham ones interchannel coupling effects and autoionization resonances play an important role at low kinetic energies. Prominent shape resonances features have been analyzed in terms of "dipole prepared" continuum orbitals and interpreted as due to a large angular momentum centrifugal barrier as well as anisotropic (nonspherical) molecular effective potential. Finally, the method has been proven numerically stable, robust, and efficient, thanks to a noniterative implementation of the time dependent density functional theory equations and suitability of the multicentric B-spline basis set to describe continuum states from outer valence to deep core states.     

The inversion phenomenon of the helical twist sense in antiferroelectric liquid crystal phase from electronic and vibrational circular dichroism

The investigation of the helical pitch and the helical twist sense for several liquid crystal compounds in antiferroelectric phase have been performed. Electronic circular dichroic (ECD) and vibrational circular dichroic (VCD) spectroscopies have proved the existence of unwound helical structure in antiferroelctric phase. Obtained results may confirm the assumption connected via the inversion phenomena in liquid crystalline chiral phase with the change of the concentration of different conformers promoting opposite handedness. Two examples of such conformers, obtained by conformational analysis, have been proposed.     

A semiempirical conformational analysis of the 3-phenyl-1,2,3-oxathiazolidine 2-oxide

An extensive conformational search for the heterocyclic compound 3-phenyl-1,2,3-oxathiazolidine 2-oxide has been carried out using the semiempirical quantum-mechanical method PM3. All torsion angles were varied in the geometry optimization procedure which led to the prediction of four distinct conformers. Barriers to internal rotation leading to conformational interconversions were also calculated. The results of the present study indicate that this five-member ring substituted heterocyclic system may be expected to exist as a mixture of stable conformers rather than a unique molecular entity.     

Camdas: An automated conformational analysis system using molecular dynamics

We present an automated conformational analysis program, CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling). CAMDAS performs molecular dynamics (MD) calculations for a target molecule and samples conformers from the trajectory of the MD. The program then evaluates the similarities between each of the sampled conformers in terms of the root- mean-square deviations of the atomic positions, clusters similar conformers, and finally prints out the clustered conformers. This MD-based conformational analysis is a broadly used method, and CAMDAS is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically from an arbitrarily given structure of the molecule. The accuracy of the program was examined using N- acetylalanine-N-methylamide, and the obtained result was consistent with that of the systematic search method. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examining only 5000 conformers. In addition, the potential-scaled method, which we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the early stage of drug design.     

Conformational and vibrational analysis with the aid of normal coordinate calculations

Many organic compounds exist as equilibrium mixtures of two or more molecular conformations, and vibrational spectroscopy can be used to obtain information about the structure of those conformations. Normal coordinate calculations are often an aid to those conformational studies and to making vibrational assignments for the different conformers. However, sometimes those calculations are partially inconclusive, and a few results are briefly discussed in which both conclusive and inconclusive results were obtained from calculations. Calculations are then applied to some 1,2-dichloro- and 1,2-dibromo-alkanes. Previous calculations on 1,2-dichloropropane and 1,2-dichlorobutane are revised, and calculations are reported for 1,2-dibromopropane, 1,2-dibromopropane-d₆, and 1,2-dibromobutane. Spectra are given for the last two of these compounds. A modified valence force field was determined for each family of 1,2-dihaloalkane that should be transferable to other members of the family.     

The gauche-trans transformation of monoethanolamine in gas phase

Monoethanolamine is a model molecule for biological systems and widespread ligand in coordination chemistry; it has a large number of isomers, of which gauche and trans are the most stable in gas and crystalline phases, respectively. The work is devoted to non-empirical study of conformational transformations of different gauche and trans isomers of individual monoethanolamine molecule. These transformations was shown to be determined by the features of formation and cleavage of intramolecular hydrogen bonds O-H?N and N-H?O and the internal rotation of substituted methyl groups. Assessments were obtained for the free energies of conformers and activation energies of their mutual transformations.     

Conformation of N,N′-bis (2,6-dimethylmorpholino), N″-dichloroacetyl phosphoric triamide: CHCl2C(O)NHP(O)[2,6(CH3)2(NC4H6O)]2. NMR and ab initio studies

Using phosphorus pentachloride as a substrate, a new carbacyclamidophosphate, N,N″-bis (2,6-dimethylmorpholino), N″-dichloroacetyl phosphoric triamide (1) has been synthesized and characterized by ¹H, ³¹P and ¹³C NMR, IR spectroscopy and elemental analysis. Due to the presence of methyl disubstituted morpholine rings and the dichloroacetamide group, several conformers can be considered for this molecule. The ³¹P{¹H} NMR spectra for the isomeric mixture of synthesized compound showed four signals with the ratio 67.1; 19.0; 12.2; 1.7, which indicates four independent conformers. The ¹H NMR spectra confirmed these results. The conformational space and the molecular geometry of the molecule in the gaseous phase have been studied using the B3LYP method of approximation, with 6-31G and 6-311++G^** basis sets.     

Variationally stable calculations for molecular systems: polarizabilities and two-photon ionization cross section for the hydrogen molecule

The variationally stable method of Gao and Starace [B. Gao and A. F. Starace, Phys. Rev. Lett. 61, 404 (1988); Phys. Rev. A 39, 4550 (1989)] has been applied for the first time to the study of multiphoton processes in molecular systems. The generalization in theory is presented, as well as the calculation of properties such as the static and dynamic polarizabilities of the hydrogen molecule and the generalized two-photon ionization cross section. The Schwinger variational iterative method [R. R. Lucchese and V. McKoy, Phys. Rev. A 21, 112 (1980)] has been applied in the achievement of the photoelectron wave function, while a Hartree-Fock representation has been used for the target. This research has been motivated by the scarceness of ab initio calculations of molecular multiphoton ionization cross sections in the literature.     

Rotationally resolved electronic spectra of 2- and 3-methylanisole in the gas phase: a study of methyl group internal rotation

Rotationally resolved fluorescence excitation spectra of several torsional bands in the S1 <-- S0 electronic spectra of 2-methylanisole (2MA) and 3-methylanisole (3MA) have been recorded in the collision-free environment of a molecular beam. Some of the bands can be fit with rigid rotor Hamiltonians; others exhibit perturbations produced by the coupling between the internal rotation of the methyl group and the overall rotation of the entire molecule. Analyses of these data show that 2MA and 3MA both have planar heavy-atom structures; 2MA has trans-disposed methyl and methoxy groups, whereas 3MA has both cis- and trans-disposed substituents. The preferred orientations (staggered or eclipsed) in two of the conformers and the internal rotation barriers of the methyl groups in all three conformers change when they are excited by light. Additionally, the values of the barriers opposing their motion depend on the relative positions of the substituent groups, in both electronic states. In contrast, no torsional motions of the attached methoxy groups were detected. Possible reasons for these behaviors are discussed.     

Permanent electric dipole moments of four tryptamine conformers in the gas phase: a new diagnostic of structure and dynamics

Rotationally resolved electronic spectroscopy in the gas phase, in the absence and presence of an applied electric field, has been used to determine the charge distribution of a cross section of the energy landscape of tryptamine (TRA). We report the magnitude and direction of the permanent electric dipole moments of the four TRA conformers GPyout, GPyup, GPhup, and Antiup in their S0 and S1 electronic states. Each dipole moment is unique, providing a powerful new tool for the conformational analysis of biomolecules in the gas phase. A comparison of the results for the different conformers of TRA reveals that the position and orientation of the ethylamine side chain play a major role in determining both the permanent and induced electric dipole moments of the different species in both electronic states.     

Sensitivity of photoelectron circular dichroism to structure and electron dynamics in the photoionization of carvone and related chiral monocyclic terpenone enantiomers

The photoelectron circular dichroism that arises in the angular distribution of photoelectrons emitted from the carbonyl group in randomly oriented pure enantiomers of carvone, and a number of carvone derivatives, is investigated by continuum multiple scattering calculations. Core ionization of carbonyl C 1s orbitals is examined for six different isopropenyl tail conformations of carvone. These show clear differences of behavior both between axial and equatorial conformations, and between the three rotational conformers of each. The pronounced dependence of the dichroism on orientation of a tail grouping, itself remote from the localized initial C 1s site, indicates the presence of long range final state photoelectron scattering effects. Analogous data for the outermost valence orbital, partially localized on the carbonyl group, are also presented. The apparently enhanced sensitivity of the dichroism exhibited in this work is discussed in terms of the particular dependence on photoelectron interference effects that is probed by the dichroism measurement and is contrasted with the usual beta parameter and cross section determinations.     

The role of conformation on electron capture dissociation of ubiquitin

Effects of protein conformation on electron capture dissociation (ECD) were investigated using high-field asymmetric waveform ion mobility spectrometry (FAIMS) and Fourier-transform ion cyclotron resonance mass spectrometry. Under the conditions of these experiments, the electron capture efficiency of ubiquitin 6+ formed from three different solution compositions differs significantly, ranging from 51 +/- 7% for ions formed from an acidified water/methanol solution to 88 +/- 2% for ions formed from a buffered aqueous solution. This result clearly indicates that these protein ions retain a memory of their solution-phase structure and that conformational differences can be probed in an ECD experiment. Multiple conformers for the 7+ and 8+ charge states of ubiquitin were separated using FAIMS. ECD spectra of conformer selected ions of the same charge states differ both in electron capture efficiency and in the fragment ion intensities. Conformers of a given charge state that have smaller collisional cross sections can have either a larger or smaller electron capture efficiency. A greater electron capture efficiency was observed for ubiquitin 6+ that has the same collisional cross section as one ubiquitin 7+ conformer, despite the lower charge state. These results indicate that the shape of the molecule can have a greater effect on electron capture efficiency than either collisional cross section or charge state alone. The cleavage locations of different conformers of a given charge state were the same indicating that the presence of different conformers in the gas phase is not due to difference in where charges are located, but rather reflect conformational differences most likely originating from solution. Small neutral losses observed from the singly- and doubly-reduced ubiquitin 6+ do not show a temperature dependence to their formation, consistent with these ions being formed by nonergodic processes.     

Raman optical activity spectra and conformational elucidation of chiral drugs. The case of the antiangiogenic aeroplysinin-1

We present the determination of the conformational properties of aeroplysinin-1 in aqueous solution by means of a combined experimental and theoretical Raman optical activity (ROA) and vibrational circular dichroism (VCD) study. Aeroplysinin-1 is an antiangiogenic drug extracted from the sponge Aplysina cavernicola which has been proved to be a valuable candidate for the treatment of cancer and other antiangiogenic diseases. Our study shows that this molecule possesses the 1S,6R absolute configuration in aqueous solution, where only two conformers are present to a significant level. We discuss in detail the relationships between the chiro-optical ROA and VCD features, and the structural properties of various energy accessible conformers are described. The present work is one of the first studies in which both ROA and VCD have been used as complementary tools for the determination of absolute configuration and dominant solution-state conformations of an unknown therapeutically significant molecule.     

Crystal and molecular structure of the sesquiterpene humulane alcohol juniferol

The spatial structure of the sesquiterpene humulane alcohol juniferol, which is represented in the crystal by two conformers, IA and IB, differing by the conformation of the C2...C9 section, has been established by the x-ray structural method. The strain energies of the conformers have been calculated by the method of molecular mechanics. The barrier to the interconversion of the conformers by rotation of the C2...C9 section has been calculated; it amounts to 7–8 kcal/mole. This value of the transformation barrier permits the assumption that the two conformers also exist in solution, their interconversion being hindered.Institute of Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Institute of Crystallography, Academy of Sciences of the USSR, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 757–762, November–December, 1990.     

Conformational behaviour, hydrogen bond competition and intramolecular dynamics in vanillin derivatives: acetovanillone and 6-hydroxy-3-methoxyacetophenone

The conformational landscape of the structural isomers acetovanillone (apocynin, AV) and 6-hydroxy-3-methoxyacetophenone (HMAP) has been investigated in a supersonic jet using Fourier transform microwave spectroscopy. Two conformers have been detected in the jet-cooled expansion for each molecule (s-cis and s-trans in AV; s-trans and a-trans for HMAP), differing in the relative orientation of the acetyl and methoxy groups. Both molecules are stabilized by O-H···O or O-H···O=C hydroxyl intramolecular hydrogen bonds, either constraining the local conformations of the methoxy group in AV, or that of the acetyl group in HMAP. Internal rotation splittings have been observed in both conformers of each molecule, originated by the acetyl group, that yield information on the influence of the intramolecular hydrogen bonds on the methyl torsion. The similar internal rotation barriers in both molecules (6.6 and 7.4 kJ mol(-1) in AV; 7.3 and 7.0 kJ mol(-1) in HMAP) suggest that the acetyl torsion is only slightly affected by intramolecular hydrogen bonding. The absence of torsional tunnellings due to the methoxy group indicates torsional barriers above 10.2 and 8.9 kJ mol(-1) for AV conformers, 10.1 and 10.4 kJ mol(-1) for HMAP. Conformational ratios and relative free energies have been estimated from relative intensity measurements of the spectral lines. Ab initio (MP2) and density functional calculations using the recent M05-2X empirical functional have been used to aid the experimental work in describing the structures, internal rotation barriers and isomerization potentials.     

Understanding glycine conformation through molecular orbitals

The four most stable C(s) conformers of glycine have been investigated using a variety of quantum-mechanical methods based on Hartree-Fock theory, density-functional theory (B3LYP and statistical average of orbital potential), and electron propagation (OVGF) treatments. Information obtained from these models were analyzed in coordinate and momentum spaces using dual space analysis to provide insight based on orbitals into the bonding mechanisms of glycine conformers, which are generated by rotation of C-O(H) (II), C-C (III), and C-N (IV) bonds from the global minimum structure (I). Wave functions generated from the B3LYP/TZVP model revealed that each rotation produced a unique set of fingerprint orbitals that correspond to a specific group of outer valence orbitals, generally of a' symmetry. Orbitals 14a', 13a', 12a', and 11a' are identified as the fingerprint orbitals for the C-O(H) (II) rotation, whereas fingerprint orbitals for the C-C (III) bond rotation are located as 16a' [highest occupied molecular orbital (HOMO)], 15a' [next highest molecular occupied molecular orbital (NHOMO)], 14a', and 12a' orbitals. Fingerprint orbitals for IV generated by the combined rotations around the C-C, C-O(H), and C-N bonds are found as 16a', 15a', 14a', 13a', and 11a', as well as in orbitals 2a" and 1a". Orbital 14a' is identified as the fingerprint orbital for all three conformational processes, as it is the only orbital in the outer valence region which is significantly affected by the conformational processes regardless rotation of which bond. Binding energies, molecular geometries, and other molecular properties such as dipole moments calculated based on the specified treatments agree well with available experimental measurements and with previous theoretical calculation.     

A theoretical approach to molecular conformational analysis

The application of ab initio molecular orbital theory to the study of molecular conformational analysis is discussed. Examples presented include methyl rotational barriers, internal rotation in 1,2-dihalogenoethanes, $\text{cis-trans}$ isomerism in 1,2-dihalogenoethylenes, rotational barriers in substituted acetones and conformational preferences in substituted hydrazines.     

Conformational behavior of dimethyl 5-methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-dioxide isolated in low-temperature matrixes

The structure of dimethyl 5-methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-dioxide (PTD) was investigated in low-temperature noble gas matrixes (Ar, Kr, Xe), amorphous solid, and the crystalline state by infrared spectroscopy and computational methods. The geometry of PTD conformers is defined by the orientation of two methyl ester groups, which may adopt pseudo-trans or pseudo-cis positions in relation to the pyrrolo-thiazole system. For both methyl ester groups, the latter arrangement was predicted by the calculations to be energetically the most favorable in the isolated molecule. The envelope form of the thiazolidine ring is present in all conformers, with the sulfur atom placed in the apex position, while the pyrrole ring is almost planar. Three types of conformers differing in the orientation of the methyl ester groups relative to the pyrrolo-thiazole system (cis/cis, trans/cis, cis/trans) were identified in the matrixes. The cis/cis forms were found to be the most stable ones in both gaseous state and argon matrixes. On the other hand, the more polar trans/cis forms were found to be stabilized in the more polarizable krypton and xenon matrixes as well as in the neat amorphous and crystalline phases. On the basis of annealing experiments, performed in argon and xenon matrixes up to 35 and 68 K, respectively, conformational changes preceding the aggregation of the compound are suggested.