Congratulations to Eric, who has just received the prestigious Goldwater Fellowship! Eric will be supported by the Goldwater Foundation during his senior year at SMU, while he conducts an environmental study focusing on removing heavy metals, including lead, cadmium, and mercury, from industrial wastewaters. Supervised by Dr. Dieter Cremer, Eric will use various relativistic programs developed by Wenli, Michael, and Dieter during the last two years at SMU, as well as the unitversity's newly acquired and improved computational facilities.
Rob is working on the Tolman rule, which plays an important role in catalysis. He can show that this rule is misleading because it is based on the assumption that CO frequencies in ttransition metal carbonyls are independent of mode-mode coupling. There are large coupling effects! This means that the Toleman rule has to be reformulated and new insights into catalysis become possible.
Wenli and Dieter are working on a new version of URVA, which will be able to use redundant or curvilinear coordinates. Their work is based on the idea that atoms move during a chemical reaction on curved paths, which are best described by curvilinear rather than rectangular (Cartesian) coordinates. One can simulate these movements also by sets of redundant coordinates. Objective of the work is to avoid path instabilities when investigating catalytic reactions. Their work will be essential for the URVA analysis of complex reactions.
Joao, Elfi, and Dieter develop the potential energy surfaces of weakly hydrogen-bonded complexes to determine exact rovibrational constants. The knowledge of these spectroscopic constants in connection with the local H-bond stretching modes will provide a much better insight into the nature of weak H-bonding.
David’s experimental results verify what Wenli and Dieter have predicted on the basis of 77^Se NMR chemical shift calculations: Selenite reacts with the dithiol BDT to form cyclic selenosulfanes, which precipitate and can be removed with mechanical means from aqueous solutions. This provides a chance to purify wastewaters from steel mills or industries working with selenium.
Marek, Thomas, Elfi, and Dieter have finished 1,3-dipolar cycloaddition study which has led a multitude of new insights. Especially, Thomas’ approach to monitor the charge transfer from the 1,3-dipole to the dipolarophile was a success because it reveals that this kind of charge transfer is essential for the labilization of the dipolarophile and the formation of radicaloid centers between which the new bonds are establish. The new insights help to understand the mechanism and the energetics of 1,3-dipolar cycloadditions at a much deeper level never reached before.
Eric is working together with Wenli and Dieter on the atomization energies of actinide hexafluorides. His studies will answer the important question to which extend atomization energies depend on spin-orbit coupling (SOC) effects. Interesting is that SOC has also some significant impact on the molecular geometry.
Rob, Elfi, and Dieter are working on the question what are the strongest chemical bonds on this globe. They have identified a number of candidates and can show that despite a large variety in the bond dissociation energies, there are several bonds that have bond strengths representative of 3.3 bonds. They are working on the publication.
Elfi presented at the local Duluth/Superior ACS section a dinner talk entitled: “What can we learn from Nature? Research connecting the in vivo with the in silicio world.” Students, faculty and guests were impressed how much chemistry can be explored with computers.
Marek is working on catalytic cycles involving Au and Rh compounds. There is the necessity to find a new way of quantifying electronic structure changes at the transition metal atom. This can be done by generalizing the curvilinear coordinates Wenli and Dieter have developed for the description of bond pseudo-rotation.
Zhanyong, Elfi and Dieter are setting up the helix analysis routines for general use on the CATCO web page after their paper has been accepted for publication in J. Mol. Model. It astonishes how difficult it is to define the secondary structure of a protein precisely. This can be done now with Zhanyong’s program HAXIS.
On April 7, Elfi presented her research on computer assisted drug design to a group of STEMPREP 12th graders. This group of extremely talented high school students has been accepted to SMU under the early action program.
Wenli and Dieter finished the analysis program for infrared intensities. This is based on the local mode intensities and the adiabatic connection scheme (ACS) between normal and local mode infrared intensities. In the case of equivalent local modes, the intensity-ACS is characterized by a catastrophe point, which helps to identify equivalent intensities in larger molecules. The intensity program reveals that H-bond stretching vibrations have large intensities, which are “dissipated” by mode-mode couplings.
On March 21, Elfi represented the research of the CATCO group as panelist at the Impact Symposium entitled: “The Power of predictions: Its promise as well as its limitation.” The event was organized by the Dedman College Interdisciplinary Institute and the Richard B. Johnson Center for Economic Studies, supported by the Embry Family Foundation. Elfi discussed that with today’s computers predictions can be made by quantum chemical calculations, which are of extreme value for the design of new materials and medicinal drugs. Often quantum chemical calculations are more accurate than experiment.
Dieter presented the J. W. Whalen Memorial Lecture at the University of Texas at El Paso (UTEP), El Paso, on March 15, 2013. He talked about “Bond curiosities throughout the periodic table.”
Elfi and Dieter wrote a review on the chemistry of the enediynes. Writing a review is even for the expert a piece of education because one is always stunned how a field can develop within a short time in such a rapid fashion. Enediynes are no longer a topic of just medicinal chemistry but also organic synthesis, mechanistic chemistry, polymer chemistry, and material sciences.
Alan and Dieter are working on pancake bonds. Typically these bonds are 3 Å and longer. Therefore the important question to be asked is whether these are really “chemical bonds.” This extends the question Alan has posed to himself: “What is the longest CC bond ever observed?
Dieter presented a seminar at TexTech University, Lubbock, on February 22, 2013, entitled: “Mercury bonding described with relativistic quantum chemistry – Report on a series discrepancy between theory and experiment.”
The spin-orbit coupling (SOC) program of Michael, Wenli, and Dieter works better than originally expected. SOC energy corrections come out very accurately and the orbital splittings caused by SOC match the most accurate calculations obtained with much more expensive methods.
Alan and Dieter are close to solving the question of the long C1C6 bond in 11,11-Dimethyl-1,6-methanoannulene. It seems that this is a result of crystal packing. In the unit cell the molecules are stapled on top of each other pressing on the bridge atoms. This leads to a widening of the bridge angle and a closing of the 1,6-interaction from 2.2 down to 1.8 Å. Alan and Dieter plan to publish these results in honor of Emanuel Vogel who pasted away last year.
Rob has finished his study of the formic acid dimer using exclusively experimental vibrational frequencies. He shows that symmetric H-bonding in the cyclic dimer is almost 2 times stronger than the H-bond of the water dimer. He has identified the normal vibrational frequency that far-infrared specialists have measured to describe H-bonding. It is strongly reduced because of mode-mode coupling and does no longer describe the true nature of H-bonding. He, Elfi, and Dieter are writing the paper summarizing these results.
Hrant and Elfi published in J. Comp. Theory Comp. their new version of the reaction path following algorithm for URVA studies which makes sure that at the beginning of a reaction the path curvature is correctly calculated. The curvature at the start of the reaction indicates whether the electronic structure of the reaction complex can be easily or hardly distorted. For example, the rotation at the ethylene bond or the rearrangement of HCN start with a high curvature.
Wenli and Dieter are working on a new version of the ACS, which will start with lambda = 1 and, in this way, can use symmetry thus avoiding a diabatic mode ordering. The reverse ACS diagrams will complement the information of the normal ACS diagrams. Any errors in the ordering of the vibrational eigenstates will quickly be found.
Marek and Elfi are working on their second chirality paper, which focuses on large chiral complexes calculated with coupled cluster methods.
CFOUR, DIRAC, GAMESS, GAUSSIAN, NWChem, MOLPRO, ORCA, and Q-Chem,
Wenli, Michael, and Dieter worked on a two-component form of the NESC program. Objective is to calculate spin-orbit coupling (SOC) including the correct splitting of the molecular orbital energies. By the end of November, the new theory and the corresponding program were finished. The NESC/SOC data match the accuracy of Dirac 4-component calculations.
A major problem with the adiabatic connection scheme is the occurrence of avoided crossings between degenerate vibrational eigenstates of different symmetry (which is obviously wrong). Wenli and Dieter worked out a procedure for rotating degenerate eigenvectors until maximum overlap criteria are fulfilled. In this way, the correct ordering of vibrational eigenstates is enforced.
Dieter presented the local modes theory at the 2012 SWTCC conference at Texas A&M, October 26 – October 28, 2012. He gave a plenary talk entitled:
“Local Vibrational Modes: A New Tool to Describe the Electronic Structure of Molecules” (see CATCO presentations)
Elfi gave a talk about “The decisive role of H-bonds in chiral discrimination unraveled by quantum chemical means” at the 2012 SWTCC.
Rob worked out a bar diagram that nicely reflects the composition of a normal vibrational mode in terms of local vibrational modes. We will routinely use these bar diagrams in the future when describing vibrational spectra.
On October 1, 2012 Elfi Kraka presented a lecture entitled “How Chemistry can Learn from Nature: - A CADD Approach to Non-toxic Enediyne Anti-tumor Drugs” at the University of Brasilia, Brasilia, Brazil.
On September 31, Dieter was invited by the Department of Physics, University of Brasilia to give a lecture entitled:
“Detailed Description of the Electronic Structure of Molecules and Chemical Bonding with Vibrational Modes” An interesting discussion about the possibilities of modern vibrational spectroscopy took place after the lecture.
Elfi and Dieter attended the Symposium for “Electronic Structure and Molecular Dynamics, IV SEEDMOL” in Pirenopolis, Brazil, September 24 – 28 where they gave plenary lectures with the titles:
“Removal of toxic contaminants from the environment – A quantum chemical study with Dirac-exact relativistic theory” (Dieter)
“Hydrogen-Bonds in Homochiral and Heterochiral Compounds Distinguished by Vibrational Spectroscopy” (Elfi)
At the same conference, Elfi and Dieter, organized and presented a workshop on:
“A new Way of Understanding Chemical Reactions: The Unified Reaction Valley Approach” (6 lectures and 6 training sessions).
The first CATCO workshop was presented. Topic was the Unified Reaction Valley Approach (URVA). In 5 days, all aspects of URVA were discussed. Contributions in form of lectures (Dieter) and in form of exercises were made by Dieter, Elfi, Marek, Thomas, Rob, Alan, Dani, and Wenli.
On August 20, 2012 Elfi Kraka presented an invited talk entitled “The Unified Reaction Valley Approach: New insights into the mechanims of 1,3-Dipolar Cycloadditions” at the Special Symposium “Exploring Potential Energy Surfaces in Quantum Chemistry. A Tribute to H. Bernhard Schlegel” held at the 244th ACS National Meeting in Philadelphia, August 19-23, 2012.
Paul and Elfi are writing up Paul's research in a paper. This is quite an accomplishment!
Rob, Wenli, Elfi, and Dieter studied the water dimer at the highest level possible. They could proof that H-bonding is much stronger than suggested by a stretching frequency of just 140 cm-1. The local mode stretching frequency is at 520 cm-1. The reduction in the frequency is a result of mass coupling, avoided crossing, and anharmonicity effects. This result is essential for Elfi and Marek’s work on chirality.
Wenli, Elfi, and Dieter are battling with the problem of getting free reaction energies as precicisely as possible in aqueous solution and to use these for pKa calculations. For smaller molecules the problem is solvable but for biomolecules it becomes a pain.
Marek and Dieter found an interesting reaction mechanism for a polymerization problem suggested by Nick, in which trivalent and tetravalent iodine plays a central role.
Wenli, and Dieter defined for the first time the intensities of the local vibrational modes. They extended the adiabatic connection schemes for the frequencies by one for the corresponding intensities. Knowing that the intensities are directly related to the atomic charges via the polar tensor, this is a much promising development. However the calculation of atomic charges from measured experimental frequencies via the local mode intensities will be a tough problem.
Paul and Elfi studied substituted phosphine dimers and found that depending on the substituent there are relatively strong stabilizing interactions via the electron lone pairs although the latter should repel rather than attract each other. Analyzing local vibrational modes and the electron density distribution a surprising through-space stabilization mechanism emerges that leads to binding energies similar to those found for H-bonded complexes. The effect will be important for crystal engineering and polymer chemistry.
Elfi and Dieter wrote up the results for the hydrogenation reactions: XH_n + H_2 --> XH_n+1 + H. X is varied through the periodic table including also heavy elements such as Bi or Pb. The curvature peaks for the chemical processes reflect the barriers of forward and backward direction quantitatively! The Hammond-Leffler postulate is verified for the first time on a quantitative basis. This shows the power of the URVA method.
Michael, Wenli, and Dieter investigated differences in the nuclear volumes of Au isotopes. They described them via the nuclear quadrupole coupling constants and the so-called quadrupole anomaly using the NESC method in connection with Coupled Cluster theory. They predict that gold complexes are ideally suited for measuring the quadrupole anomaly and getting in this way information on the nuclear volume (we are talking here about a radius of 5.43 fm = 5.43 x 10^-15 meter!)
Thomas has found a solution for generating snapshots along the reaction path much more efficiently than was previously done by Marek. He has programmed Avogadro with the help of Geoffrey Hutchinson. This will reduce the work to present and analyze URVA results tremendously.
Alan is battling to describe the “longest CC” bond ever observed. This is the 1,6 bond of 1.8 Å in one of the substituted methanoannulenes. The work is done in honor of Professor Emanuel Vogel, who passed away last year. He was one of the supervisors of Dieter (see Dieter’s scientific tree). DFT, Coupled Cluster, Multireference CC, REKS, CASSCF, CASPT2 – no method can reproduce the X-ray geometry. The interaction distance seems to depend on environmental effects.
Elfi presented her work (done together with Marek) on chirality at the Forth Worth International Chirality meeting. She investigated the question why biomolecules are preferentially homochiral rather than heterochiral. Utilizing the local modes and describing H-bonding, Elfi and Marek have an answer.
This is the summer of writing up results. The number of publications submitted or written up extends largely what was done in the first two years. However the publications are largely a result of what has been done in the first years.
Dani arrived. Dani has already some experience in REKS-DFT and TD-DFT, which he can bring in. He will use the adiabatic connection scheme to simplify the interpretation of vibrational spectra.
Eric and Dieter finished the work on the actinidehexafluorides. Eric compared both the old NESC and the SMU-NESC method. The latter contrary to the former provides reliable results, which is very important when second order response properties are calculated.
Marek and Elfi investigated the question how chiral molecules were formed in the early stages of this globe. Why are most biomolecules homochiral rather than heterochiral? Their answer is that chiral molecules are generated in the course of complex formations. They demonstrate that H-bonding plays an important role. By analyzing H-bonding they can predict the chirality of the complexes formed.
Wenli and Dieter have found a second criterion how to get a unique force constant matrix for the Wilson FG formalism. The important result is that local mode force constants do not depend on the way Cartesian force constants are transformed into internal coordinate force constants.
David, Wenli, and Dieter have found a way to detect Se in ppb concentrations, to complex it, and precipitate it. A paper is in preparation. David and Dieter have developed a project to extend the work for the investigation of arsenic in drinking water.
Dieter gave a talk on the relativistic work and its application to environmental questions. It is a wonderful idea to hear what our colleagues in physics, math, and biology are doing.
Dieter and David have joined forces for designing and synthesizing organic tweezers molecules suitable to remove contaminants from the environment. Dieter’s works focuses on mercury contaminations. Laboratory results suggest that organic tweezers can clean waters from Hg in a very efficient way.
Dieter wrote a long review article on Configuration Interaction (CI) and Quadratic Configuration Interaction (QCI) theory. He described the various development steps of CI and the history of Pople’s QCI. He provided a balanced view on the scientific dispute between Pople and Paldus, the limitations of QCI, and how Zhi He and Dieter overcame these problems.
Wenli and Dieter achieved another breakthrough by proofing that the local modes of Konkoli and Cremer are the true counterparts of the normal vibrational modes. The missing link between the two sets of force constants is the compliance matrix of Decius. Wenli and Dieter worked out the adiabatic connection schemes between normal and local modes. With the local modes and the adiabatic connection schemes Chemists have now a powerful tool in their hands to describe bonding, changes in bonding, and the reorganization of electronic structure during chemical reactions.
Elfi and Dieter organized the 24. Austin Symposium on Molecular Structure and Dynamics at Dallas (ASMD@D). 80 participants from 18 different countries attended an exciting conference. Essential for the success was the fact that presentations, discussions, and lunches took place all at the same locality. The Texan hospitality and the organization were praised by the participants. Dean Quick and Dean Tsutsui provided essential support without the ASMD2D would not have been so successful. The CATCO group made an important step to increase the visibility of SMU at an international level.
Wenli and Dieter proofed that the compliance constants of Decius are nothing else but the reciprocals of the local mode force constants of Decius. Rob and Elfi confirmed this for some 40 organic molecules by calculating the corresponding values. This is a huge step forward in the description of bonding.
Michael, Wenli, and Dieter finished the work on nuclear contact densities, which enables the calculation of Mössbauer shifts. Mössbauer spectroscopy has an increasing importance in environmental chemistry because one can detect heavy metal contaminations down to the ppb range. The calculated Hg-Mössbauer shifts are in excellent agreement with the observed values.
Michael, Wenli and Dieter worked out the relativistic corrections for hyperfine structure constants using the NESC methodology and programs they had worked out in 2011. The calculation of these constants for heavy metal means is an important step for the detection of contaminants in the environment using analytical means such as EPR.
Wenli and Dieter finished the work on the cyclopentadienyl cation, which is a molecule without structure because the inherent Jahn-Teller effect. The C atoms perform circular motions, which lead to bond-pseudorotation. Thanks to the curvilinear coordinates of Dieter and Wenli, the bond-pseudorotation surface of four substituted cyclopentadienyl cations expanded in terms of curvilinear coordinates could be determined for the first time. The deformation coordinates reveal that the pseudo-Jahn-Teller effect is much more important for cyclopentadienyl cations than the Jahn-Teller effect.
Over X-mas Elfi and Dieter wrote up the description of H-bonds with the help of local modes based on Marek’s calculations. The local H-bond stretching force constant turns out to be a reliable and useful descriptor of the H-bond strength. For the first time covalent and pure electrostatic H-bonds can be distinguished by combining the local mode properties with the Cremer-Kraka criteria for covalent bonds. This will be a powerful tool for the investigation of H-bonfs in biomolecules.
Wenli, Michael, and Dieter developed additional ways of getting accurate second derivatives for the renormalization term and matrix U that connects the large and the pseudo-large component of the modified Dirac equation.
Rob gave his research presentation. He could show that the stability of carbenium ions is effectively increased by Cl and F, but less by Br and I. He also described bonding in halonium ions and between carbon and chalcogen atoms. There is a stunning similarity in the bonding mechanism of CX and CE bonds. The pi-contributions become significantly weaker for the higher homologues.
Michael demonstrated that the response theory for second order properties within relativistic theory can be elegantly formulated within NESC. The NESC second derivative program works accurately. Wenli wrote some 3000 lines of FTN coding for this purpose.
Wenli, Michael, and Dieter worked out the second derivatives for the relativistic NESC method and programmed them within COLOGNE. To get the second order response properties on needs, besides the electronic states, also the positronic states of the Dirac equation contrary to some claims in the literature.
Rob is finishing his work on CX bonding (X = F, Cl, Br, I).
Elfi gave a talk on Anticancer Drugs at UTA.
CATCO carried out the first workshop for high school students. From 9 am to 6 pm, students of the School of Science and Engineering, Yvonne A. Ewell Townview Magnet Center, Dallas, were introduced into quantum chemical calculations and quantum chemical research (see Time Schedule for Workshop).
Wenli and Dieter finally solved the basic secret of the compliance constants: They can be related to local modes.
Zhanyong, Elfi, and Dieter give the reaction library a new form.
Marissa calculated the pseuorotational surface of adenosine and demonstrated the influence of H-bonding.
Eric showed that picture change and finite nuclei have little influence on molecular properties of actinide hxafluorides such as geometry and vibrational frequencies, however a large influence on the energy.
Dieter presented at the SimOC conference in Vigo, Spain, a talk on Reaction Mechanism.
Elfi presented a talk on Reaction Design and the Formation of Allenylcarbene at the WATOC 2011, Santiago del Compostella, Spain.
Dieter presented at the WATOC 2011, Santiago del Compostella, Spain, the work on the NESC energy gradients.
Wenli derived an improved one-step solution of the Sylvester equation in connection with the NESC gradient.
Elisabeth is investigating the conformational flexibility of cytidine.
Wenli and Dieter published the basic paper on Jahn-Teller surfaces spanned by deformation coordinates.
Wenli, Michael, and Dieter publish the new NESC algorithm and the analytical energy derivatives of the relativistic NESC equations; this leads to a big step forward in correctly calculating the molecular properties of molecules with heavy atoms, which is absolutely necessary for the catalytic studies of the CATCO group.
Wenli and Dieter finished their work on deformation coordinates. For the first time Jahn-Teller surfaces and phenomena such as bond pseudorotation can be presented with a set of natural deformation coordinates in this way avoiding the tedious (and sometimes unsolvable) problems with normal coordinates. Bond pseudorotation in the cyclopropyl radical cation, cyclobutadiene, and other molecules was described.
Zhanyong is working on the APSA program and webpage. The first paper is about to get finalized.
Elfi has introduced the improved version of the URVA program that uses a larger step size but nevertheless resolves avoided crossings with the help of perturbation theory.
Rob gave a group seminar on the basics of vibrational spectroscopy. View the Presentation.
Eric has started to calculate uranium hexafluoride with high precision using NESC.
The task of explaining the Z-E-isomerization of the indolin-2-ones suggested by Ed Biehl’s group turns out to become a major research project. The reaction proceeds in 7 hours at room temperature. How can rotation at an ethene-type double bond become so easy? Elfi and Dieter seem to have found the solution.
Wenli, Michael, and Dieter have made a big step in getting relativistic corrections as accurate as a four-component Dirac description.
Rob, Elfi, and Dieter are working on a new justification of the adiabatic vibrational modes. There is a chance to solve this problem once and for all.
Wenli and Dieter managed to solve an important Jahn-Teller problem: How can one describe bond pseudorotation in cyclic systems such as the cyclopentadienyl cation or the cyclopropane radical cation. There is a lot of potential of extending their ideas to bond shifting in annulenes.
Professors Elfi Kraka and Dieter Cremer have designed an anti-cancer drug model that could lead to safe, more effective cancer treatments. The design involves natural substances, called enediynes, produced by microorganisms found in Texan and Argentine soils that, after slight but crucial modification, target tumor cells rather than healthy ones.
They conducted the research with the assistance of a team of graduate students from all over the world during a longer time period.
"Often cancer patients suffer severely from cancer treatments based on chemotherapy," Kraka said. “This new drug model could potentially help numerous people avoid illnesses and potentially fatal health complications that stem from side-effects often accompanying other drug treatments."
Their research was published in the American Chemical Society’s Journal of Physical Chemistry B and is recognized by the organization as a potentially major breakthrough in cancer research.
The breakthrough that Professors Kraka and Cremer and their team have made could have a tremendous impact on the treatment of one of the most significant diseases of our times. There are very few homes that would not be affected by this potentially groundbreaking drug model as families across the country and throughout the world can claim a relative who has suffered from this terrible disease.
For years, scientists have investigated substances produced by microorganism that naturally occur in soil. “Microorganisms have learned for 2 billion years longer than we how to fight toxic bacteria and viruses and in this time they have developed compounds such as the enediynes. Enediynes are the masterpieces of natural ingenuity and share a common mechanism, namely to cut like a scissors through the DNA of a cell. ” Kraka points out. “We have to learn from nature, however not blindfolded, but adjust nature’s design to our needs.” The natural enediynes kill both cancer and healthy cells, which limits their effectiveness as anti-cancer drugs. Nevertheless, one has used for example in Japan enediynes already as antitumor drugs at the cost of serious side effects. “If a patients has no other choice, he or she will even take an otherwise toxic drug to stop cancer growth”, Kraka says.
The researchers learned through computer-assisted drug design that by combining enediynes with other substances called amidines also found in microorganism, they can form agents that target preferably acidic environments. Since cancer cells generate an acidic environment whereas normal cells have a slightly basic environment, only the cancer cells will be destroyed by these so called dynemicin-amidines (DADs) drug candidates.
Researchers are currently seeking pharmaceutical companies that would be interested in the design of the first nontoxic enediyne antitumor drugs based on the DAD principle.