The Molecular Physics Laboratory, historically, has evolved around the Raman spectrometer. At present there are three research groups active in the laboratory, headed by Prof. Folke Stenman, Doc. Niklas Meinander, and Doc. Berit Mannfors. The research interests of Doc. Tom Sundius closely associates him with the laboratory. Dr. Sisko Maria Eskola, Doc. Kim Palmö (U. of Michigan) and Doc. Lars-Olof Pietilä (VTT), who did their PhD theses in this laboratory, are also actively engaged in the research projects of the laboratory. Graduate students working in the laboratory were Dr. Olli-Pekka Sievänen, M.Sc. Kari O. Eskola, Lic. Phil. Stefan Söderholm, M.Sc. Johanna Blomqvist, and M.Sc. Virpi Korpelainen. Several collaborative projects with research groups both in Finland and abroad are going on. Doc. Berit Mannfors has worked at The University of Michigan during all of 1999.

The following theses (one PhD, two Lic. Phil. and four M.Sc.) were completed under the supervision of Folke Stenman during 1999: PhD-thesis: "Numerical investigations in spectral and signal space of Raman spectra and of simulated ion bombarded surfaces" by Olli-Pekka Sievänen, Lic. Phil.- theses: "Protein folding problem. An algorithmic lattice model approach" by Jarmo Alander and "EMFi-actuator: Vibro-acoustical consideration" by Ari Saarinen, M.Sc.-theses: "Polysyklisten aromaattisten hiilivetyjen infrapunaspektrit" by Erkki Helo, "10000 metrin juoksun vauhdinjaon optimointi" by Pekka Kiviharju, "Lyhytketjuisten aminohappojen ramanspektrit" by Jukka Lönnqvist, and "Pyreenin ramanspektri" by Juha-Pekka Repo.

A 2 h/week course presenting the research being done in the laboratory was offered for the fourth time during the autumn term. Courses on molecular physics, molecular spectroscopy, spectroscopy of liquids, intermolecular forces, molecular modeling, optics and digital spectral analysis are given at more or less regular intervals as part of the senior undergraduate and graduate program of the department.

Folke Stenman and Niklas Meinander




Niklas Meinander

Two-dimensional potential energy surfaces are optimized to the observed vibrational levels of coupled large amplitude vibrational modes of small ring molecules. The potential energy surface determines the equilibrium conformation of the molecule. The molecules are studied both in the electronic ground state and in electronically excited states. This is a collaboration with prof. J. Laane at the Department of Chemistry of Texas A & M University, where the experimental work is carried out.

Two papers on this work were published in 1999 [1,2] and a manuscript submitted. [3] The ongoing work was presented at one conference during the year. [4]

1. S. Sakurai, N. Meinander, Paul Sagear, Deb N. Nath, and J. Laane, "Far-infrared spectra and two-dimensional potential energy surfaces for the out-of-plane ring vibrations of tetrahydrofuran-3-one in its S0 and S1(n,p*) electronic states". J Amer Chem Soc 121 (1999) 5056-5062

2. J. Laane, S. Sakurai, T. Klots, N. Meinander, K. Morris, W. Y. Chiang, and E. Bondoc, "Vibrational potential energy surfaces for phthalan and 1,3 benzodioxole in their S0 and S1(p,p*) states". J Mol Struct 480-481 (1999) 189-196

3. J. Laane, E. Bondoc, S. Sakurai, K. Morris, N. Meinander, and J. Choo, "Spectroscopic Determination of the Vibrational Potential Energy Surface and Conformation of 1,3-Benzodioxole in Its S(p,p*) Excited State. The Effect of the Electronic Transition on the Anomeric Effect". J Am Chem Soc, Accepted 2000

4. S. Sakurai, K. Morris, N. T. Meinander, E. Bondoc, and J. Laane, "Far-Infrared, Ultraviolet, Raman and Laser Induced Fluorescence Spectra and Vibrational potential energy surfaces of 1,3-benzodioxole. Evidence for the Anomeric Effect in Ground and Excited Electronic States". American Chemical Society Meeting, Anaheim, California, March 1999.



Niklas Meinander, Stefan Söderholm and Yrjö Roos

The glass transition in amorphous sugars is studied using Raman spectroscopy. This is a collaboration with Dr. Yrjö Roos at the Department of Food Technology, University of Helsinki (Elintarviketeknologian laitos). The project is part of a large collaboration financed by EU [1] which aims at understanding the role of sugar as a food preservative. Lic. Phil. Stefan Söderholm will write his PhD-thesis on the results of this project.

The Raman spectra of the amorphous phase of glucose and fructose have been measured as a function of the amount of water in the sample [2] and as a function of temperature. [3] The project has been presented at various meetings during the year. [4-7]

1. Commission of the European Communities, Agriculture and Fisheries (FAIR) specific RTD programme, CT96-1085, Enhancement of Quality of Food and Related Systems by Control of Molecular Mobility

2. Stefan Söderholm, Yrjö H. Roos, Niklas Meinander and Matti Hotokka, Raman spectra of fructose and glucose in the amorphous and crystalline states, J Raman Spectrosc 30 (1999) 1009-1018

3. S. Söderholm, Y. H. Roos, N. Meinander and K. Steinby, Temperature dependence of the Raman spectrum of glucose in the glassy and rubbery states, J Raman Spectrosc, submitted

4. S. Söderholm, Y. H. Roos and N. Meinander, "Normal mode analysis of the spectra of glucose and fructose", Proc. of the XXXIII Annual Conference of the Finnish Physical Society, Turku, Finland, March 4 - 6, 1999, p. 8.13

5. S. Söderholm, Y. H. Roos and N. Meinander, "Molecular Mobility in Biopolymers Determined using Raman Spectroscopy", Workshop on Molecular Mobility in Foods, Arranged by The Workshops Arrangements Committee of the European Commission Contract Enhancement of Quality of Food and Related Systems by Control of Molecular Mobility (ERBFAIRCT961085), Camogli, Italy, April 6-7, 1999, p. 17 in the Book of Poster Abstracts

6. S. Söderholm, Y. H. Roos, N. Meinander and M. Hotokka, "Characterization of Carbohydrates Using FT-Raman Spectroscopy", 1999 IFT Annual Meeting, Chicago, Il., USA, July 24-28, 1999, Poster 15-11, p. 28 in the Technical Program Book of Abstracts

7. S. Söderholm, N. Meinander and Y. H. Roos, "Molecular Mobility in Biopolymers Determined using Raman Spectroscopy", The 12th Internat. Conference on Fourier Transform Spectroscopy, Tokyo, Japan, Aug 21-27, 1999, p. TU55 in the Book of Abstracts. In Fourier Transform Spectroscopy, Twelfth Int. Conf., Ed. by Koichi Itoh and Mitsuo Tasumi, Waseda University Press, Tokyo, Japan, 1999, pp. 515-516



Johanna Blomqvist, Virpi Korpelainen, Berit Mannfors and Tom Sundius

In this project atomistic simulations (quantum mechanics and force field-based methods) are used for prediction of molecular properties based on structure in different types of molecular systems. The results obtained also are utilized in the investigation and development of (spectroscopic and molecular mechanics) force field methods. The research, described below, is divided between two research groups.



Johanna Blomqvist, Virpi Korpelainen and Berit Mannfors

This project aims at the construction of physical potential energy functions for force field-based simulations of polymers, catalysts, drugs, and biologically active species. The computational methods used are based on quantum mechanics, molecular mechanics, molecular dynamics, and statistical methods like Monte Carlo simulations. Experimental data consist of Raman and infrared vibrational spectra and structure determinations by X-ray crystallography. Major applications are various synthetic polymers and biopolymers. Theoretical calculations have been performed using the facilities at the Center for Scientific Computing (CSC/Tieteellinen laskenta Oy., Espoo, Finland) and at the University of Michigan.

In 1999 the research has been performed in close collaboration with prof. Samuel Krimm (University of Michigan, USA, proteins) and with Dr. Lars-Olof Pietilä (VTT Chemical Technology, synthetic polymers). One of the members of the group (B.M.) has worked in prof. Krimm's laboratory since January 1999. During 1999 the group's research has been divided into two parts: computational studies of synthetic polymers and development of new potential energy functions for biopolymers.

In 1999 the quantum mechanical and force field study on model molecules for polyesters with weakly interacting carboxyl groups was completed and published [1]. In this study serious disagreements were found between the quantum mechanical and the commonly available PCFF (Polymer CFF) force field results on the rotational behaviour of certain types of chemical bonds. A similar study on model molecules for biodegradable poly(lactic) and polyglycolic acids has been accepted for publication [2]. Corresponding calculations have been performed also for esters with tartaric units and fluoroalkanes [3-4]. Observed deficiences in the PCFF force field were corrected by reoptimizing the torsion potential of PCFF [1-4]. This modified PCFF was further utilized to generate the correct conformational statistics of the studied polymer chains for calculation of single chain properties of various polyesters by the RIS Metropolis Monte Carlo method [5-7]. Calculations utilizing the Amorphous Cell method by Molecular Simulations Inc., and the modified PCFF force field, have also been performed for polyfluorides and biodegradable polyesters [8,9]. These calculated results predict correctly the biodegradability of the studied polyesters [8]. Also the calculated structure of amorphous polyvinylidenefluoride is in excellent agreement with the latest X-ray crystallographic results [9].

In the other project new molecular mechanics electrostatic models have been developed for amino acid side chains containing hydroxyl groups [10,11]. Induced effects (polarization), which have been explicitly included in the model, have been found to be extremely important for a good description of the ab initio electric potentials of the studied dimers and complexes. Also for the hydrogen-bonded structures of the studied molecular systems the polarizability model has worked excellently [10,12]. In fact, polarizable models have been found to be the only electrostatic models that can reproduce the electric potentials of molecular systems when intermolecular distances and configurations vary widely, as in molecular dynamics and Monte Carlo simulations.

Concerning other studies during 1999, the force field study for model molecules of olefins was accepted for publication [13].

1. J. Blomqvist, L. Ahjopalo, B. Mannfors and L.-O. Pietilä, Studies on Aliphatic Polyesters I: Ab Initio, Density Functional and Force Field Studies of Esters with One Carboxyl Group, J Mol Struct (Theochem) 488 (1999) 247-262

2. J. Blomqvist, B. Mannfors and L.-O. Pietilä, Studies on Aliphatic Polyesters. Part II. Ab Initio, Density Functional and Force Field Studies of Model Molecules with Two Carboxyl Groups, J. Mol. Struct. (Theochem), accepted for publication.

3. V. Korpelainen, B. Mannfors and L.-O. Pietilä, Studies on Aliphatic Polyesters. Part III. Ab Initio, Density Functional and Force Field Studies of Esters with Tartaric Units, manuscript in preparation

4. V. Korpelainen, B. Mannfors and L.-O. Pietilä, Ab Initio, Density Functional and Force Field Studies of Fluoroalkanes. Conformational Statistics in Polyvinylidenefluoride, Polyvinylfluoride and Teflon, manuscript in preparation.

5. J. Blomqvist, B. Mannfors and L.-O. Pietilä, RIS Metropolis Monte Carlo Studies of Some Aliphatic Main Chain and Side Group Polyesters, Polymer, submitted for publication.

6. J. Blomqvist, RIS Metropolis Monte Carlo Studies of Poly(L-lactid), Poly(L,D-lactid)

and Polyglycolic Acids, manuscript in preparation.

7. V. Korpelainen, B. Mannfors and L.-O. Pietilä, RIS Metropolis Monte Carlo Studies of Polyesters with Tartaric Units, manuscript in preparation.

8. J. Blomqvist, B. Mannfors and L.-O. Pietilä, Amorphous Cell Studies of Poly(L-lactid), Polyglycolic, Poly(L,D-lactid) and Poly(lactide-co-glycolide) Acids, manuscript in preparation.

9. K. Jokela, V. Korpelainen, R. Serimaa, B. Mannfors, and S. Vahvaselkä, The Liquid Structure of Polyvinylidenefluoride by Molecular Modelling and X-Ray Scattering, manuscript in preparation.

10. B. Mannfors, K. Palmö and S. Krimm, A New Electrostatic Model for Molecular Mechanics Force Fields, manuscript in preparation.

11. B. Mannfors, K. Palmö and S. Krimm, A Molecular Mechanics Electrostatic Model for Alcohols, manuscript in preparation.

12. N. Mirkin, B. Mannfors, K. Palmö and S. Krimm, A Polarizable Electrostatic Model for Hydrogen Bonding of Peptide Groups, calculations in progress.

13. B. Mannfors, T. Sundius, K. Palmö, L.-O. Pietilä and S. Krimm, Spectroscopically Determined Force Fields for Macromolecules. Part 3. Alkene Chains, J Mol Struct, accepted for publication.



Tom Sundius and Igor Ignatyev*

Structures of tolyl C6H4+CH3, benzyl C6H5CH2+ ions and their Si-substituted analogues, i.e. silatolyl C6H4+SiH3 and silabenzyl cations C6H5SiH2+ have been optimized at the B3LYP/6-31(d,p) level of theory. For both C7H7+ and C6H7Si+ systems the structures with the positive charge localized at the exocyclic carbon and silicon are 44 and 48 kcal/mole more stable than the corresponding structures with the positive charge localized at the benzene ring. The barrier height for the interconversion of the ortho- and meta-isomers of the tolyl cation, i.e. 1,2-H shift, is 49 kcal/mol and that of the silabenzyl cation is 57 kcal/mol. The transition states for H-shifts from methyl and silyl groups to the positive charge center at the phenyl ring leading to benzyl and silabenzyl cations have been found. The barrier height of this rearrangement for the tolyl cation (26 kcal/mol) is sufficiently higher than that of the silatolyl cation (9 kcal/mol). Stationary points on the path leading from the benzyl cation to the global minimum of the C7H7+ system, i.e. tropylium cation, were also found. The experimental data were rationalized taking into account the theoretical results obtained.

* Russian Academy of Sciences, St. Petersburg