Chemistry 4560/5560 Molecular Modeling Fall 2014 1 Final Exam Name:………………………………………. User’s guide: 1. Read questions carefully and make sure you understand them before answering (if not, ask). 2. Answer only the question that is asked, not a different question. 3. Unless directed otherwise (e.g. offered a short answer such as Yes/No) answer in a complete, grammatically meaningful English sentences. 4. Formulate your answers clearly and precisely. 5. Write legibly. Example: Q: What is Huckel theory? A: Huckel theory is an empirical molecular orbital method designed for electronic structure calculations for conjugated hydrocarbons. 1. Potential Energy Surface (PES). a. Potential energy surface (PES) is one of the central concepts in molecular modeling. Define PES: b. Can PES be experimentally measured? (Yes/No) c. What are the so called ‘stationary points’ on the PES surface?
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Chemistry 4560/5560 Molecular Modeling Fall 2014 · Chemistry 4560/5560 Molecular Modeling Fall 2014 2 d. Give specific examples of stationary points and briefly explain why they
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Chemistry 4560/5560 Molecular Modeling Fall 2014
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Final Exam Name:……………………………………….
User’s guide: 1. Read questions carefully and make sure you understand them before answering (if not, ask). 2. Answer only the question that is asked, not a different question. 3. Unless directed otherwise (e.g. offered a short answer such as Yes/No) answer in a complete, grammatically meaningful English sentences. 4. Formulate your answers clearly and precisely. 5. Write legibly. Example: Q: What is Huckel theory? A: Huckel theory is an empirical molecular orbital method designed for electronic structure calculations for conjugated hydrocarbons.
1. Potential Energy Surface (PES).
a. Potential energy surface (PES) is one of the central concepts in molecular modeling. Define
PES:
b. Can PES be experimentally measured? (Yes/No)
c. What are the so called ‘stationary points’ on the PES surface?
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d. Give specific examples of stationary points and briefly explain why they are important:
e. For a model molecule (e.g. in Gaussian), conceptually describe how a stationary point on the
PES is found:
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f. Stationary points can be characterized by calculation of vibrational frequencies. For the
examples of the stationary points on the PES you gave above, explain how.
g. Does it make sense to calculate (harmonic) vibrational frequencies at other than stationary points
of the PES? Explain you answer.
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2. In the following, you will describe in general terms (no specific keywords etc. needed) the
sequence of steps and types of calculations that you need to obtain a desired molecular
property.
For example:
Q: NMR chemical shift of molecule X with respect to TMS
A: 1. Optimization of X
2. Calculation of NMR shieldings for X
3. Optimization of TMS
4. Calculation of NMR shieldings for TMS
5. Subtraction of TMS shieldings from those of the molecule X yields the desired chemical
shifts.
For following reaction
CH3Cl + OH ⇌ CH3OH + Cl
a. The reaction enthalpy at 450K and 10 atm pressure.
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b. The equilibrium constant at the same T and p:
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c. The forward rate of the reaction at the same T and p
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d. The isotopic effect of deuteration of CH3Cl (i.e. CH3Cl becomes CD3Cl where D stands for
deuterium) on the rate of the reaction. Isotopic effects means how the reaction rate changes upon
the isotopic substitution.
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3. When using various computational levels, it is important to pay attention to their
availability. This is an excerpt from the Gaussian manual:
AVAILABILITY
Analytic energies and gradients for CCD and CCSD, numerical gradients for CCSD(T), and numerical
frequencies for all methods. The restricted open-shell (RO) method is available for CCSD and CCSD(T)
energy calculations.
Explain the meaning and practical implications of the availability of
a. Analytic gradients:
b. Analytic frequencies:
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c. Numerical gradients:
d. Numerical frequencies:
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5. The Hartree-Fock (HF) theory forms the basis of the entire computational chemistry (as
well as computational physics). Yet, as you know, HF theory provides neither correct, nor
even very accurate solution to the molecular electronic structure problem (= molecular
Schrodinger equation).
a. Why, then, is HF theory so important?
b. Despite its central importance, however HF level is rarely used in computational chemistry.
What is the major drawback of HF that demands use of different (higher-level) methods?
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c. Even though HF equations significantly simplify the multi-electron problem, they still cannot
be solved in the closed form. Rather, they require a procedure known as the Self-Consistent Field
(SCF). Describe how this procedure works:
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d. There are several incarnations of HF methodology in practical use. In particular, we distinguish
between the so-called ab initio HF and semi-empirical HF methods. Describe the difference
between them.
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f. Furthermore, HF can be restricted (RHF) or unrestricted (UHF). For what kinds of problems are
RHF calculations appropriate, and for what problems UHF ones are used? Explain briefly and
illustrate the RHF and UHF electron configuration with a sketch.
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6. Basis sets
a. Molecular orbitals (MO) are generally described as a linear combination of atomic orbitals
(MO-LCAO). The AO’s are in turn expressed in terms of (atomic) basis functions. The Slater-type
orbital (STO) is considered to correct form of the atomic basis function. Why?
b. What is the difference, if any, between the Slater-type orbital (STO) and Slater determinant?
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c. STOs are virtually never used in actual basis sets. What types of functions are used instead and
why?
d. This is a piece of the Gaussian calculation output:
There are 297 symmetry adapted basis functions of A symmetry.